Starting phenix.real_space_refine on Fri Mar 6 03:45:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oqy_13034/03_2026/7oqy_13034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oqy_13034/03_2026/7oqy_13034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oqy_13034/03_2026/7oqy_13034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oqy_13034/03_2026/7oqy_13034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oqy_13034/03_2026/7oqy_13034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oqy_13034/03_2026/7oqy_13034.map" } resolution = 2.61 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= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Fe 3 7.16 5 Zn 8 6.06 5 Mg 1 5.21 5 S 140 5.16 5 C 17800 2.51 5 N 4836 2.21 5 O 5244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28032 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6984 Classifications: {'peptide': 875} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 822} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 8718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8718 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1051} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3024 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2039 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1421 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 175} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 856 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 987 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 608 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 690 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "N" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 534 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "P" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 376 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "Y" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'F3S': 1} Classifications: {'undetermined': 1} 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: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 427 SG CYS A 58 51.440 75.409 58.203 1.00 99.56 S ATOM 447 SG CYS A 61 51.843 71.624 57.653 1.00 96.69 S ATOM 489 SG CYS A 68 54.084 73.455 60.135 1.00 87.51 S ATOM 736 SG CYS A 98 86.427 81.994 23.952 1.00122.96 S ATOM 767 SG CYS A 101 84.630 79.035 22.262 1.00124.29 S ATOM 1154 SG CYS A 146 88.475 79.210 22.330 1.00134.49 S ATOM 1177 SG CYS A 149 86.290 81.435 20.140 1.00136.57 S ATOM 4560 SG CYS A 575 118.163 37.912 103.565 1.00 79.02 S ATOM 4600 SG CYS A 580 114.810 37.995 103.990 1.00 67.50 S ATOM 15221 SG CYS B1060 59.135 62.746 46.290 1.00 83.18 S ATOM 15244 SG CYS B1063 61.494 65.402 46.204 1.00 81.50 S ATOM 15375 SG CYS B1078 58.252 65.740 47.958 1.00 97.82 S ATOM 20141 SG CYS D 183 101.510 55.703 136.503 1.00 33.83 S ATOM 20316 SG CYS D 206 100.947 54.351 132.141 1.00 30.60 S ATOM 20340 SG CYS D 209 104.453 51.316 134.631 1.00 39.33 S ATOM 20294 SG CYS D 203 98.374 50.855 135.816 1.00 26.41 S ATOM 26090 SG CYS N 7 82.059 68.606 125.881 1.00 15.43 S ATOM 26114 SG CYS N 10 81.465 65.520 128.196 1.00 19.36 S ATOM 26377 SG CYS N 44 85.060 66.590 127.087 1.00 18.89 S ATOM 26383 SG CYS N 45 83.083 68.407 129.631 1.00 19.95 S ATOM 26611 SG CYS P 6 59.193 104.635 111.898 1.00 68.49 S ATOM 26761 SG CYS P 26 56.892 106.336 112.093 1.00 77.41 S ATOM 26786 SG CYS P 29 59.542 107.834 112.775 1.00 81.37 S ATOM 27331 SG CYS Y 4 135.606 123.465 61.403 1.00114.11 S ATOM 27449 SG CYS Y 20 134.033 121.216 58.368 1.00128.01 S ATOM 27776 SG CYS Y 63 119.614 63.090 80.396 1.00 48.53 S ATOM 27800 SG CYS Y 66 118.898 66.777 79.665 1.00 50.77 S ATOM 27940 SG CYS Y 83 120.617 65.833 82.843 1.00 45.55 S ATOM 27961 SG CYS Y 86 116.949 64.987 82.402 1.00 48.87 S Time building chain proxies: 5.54, per 1000 atoms: 0.20 Number of scatterers: 28032 At special positions: 0 Unit cell: (160.58, 151.9, 162.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Fe 3 26.01 S 140 16.00 Mg 1 11.99 O 5244 8.00 N 4836 7.00 C 17800 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S D 301 " pdb="FE4 F3S D 301 " - pdb=" SG CYS D 203 " pdb="FE3 F3S D 301 " - pdb=" SG CYS D 209 " pdb="FE1 F3S D 301 " - pdb=" SG CYS D 183 " pdb="FE1 F3S D 301 " - pdb=" SG CYS D 206 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 71 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 68 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 61 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 58 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 149 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 101 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 98 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 580 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 575 " pdb="ZN ZN A 904 " - pdb=" ND1 HIS A 582 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" NE2 HIS B1081 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1060 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1063 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1078 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 29 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 6 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 26 " pdb=" ZN Y 101 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 20 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 4 " pdb=" ZN Y 102 " pdb="ZN ZN Y 102 " - pdb=" SG CYS Y 66 " pdb="ZN ZN Y 102 " - pdb=" SG CYS Y 83 " pdb="ZN ZN Y 102 " - pdb=" SG CYS Y 86 " pdb="ZN ZN Y 102 " - pdb=" SG CYS Y 63 " Number of angles added : 24 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6590 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 46 sheets defined 39.5% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 86 through 96 removed outlier: 3.628A pdb=" N ASP A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.854A pdb=" N ARG A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 142 removed outlier: 3.845A pdb=" N LYS A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 233 through 255 removed outlier: 4.065A pdb=" N ASP A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 278 removed outlier: 4.135A pdb=" N LEU A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.753A pdb=" N LEU A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.974A pdb=" N TYR A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.519A pdb=" N SER A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.637A pdb=" N LYS A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY A 571 " --> pdb=" O ILE A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 610 through 620 Processing helix chain 'A' and resid 620 through 643 removed outlier: 4.062A pdb=" N PHE A 632 " --> pdb=" O MET A 628 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.684A pdb=" N ASP A 650 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 651 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 652' Processing helix chain 'A' and resid 654 through 681 removed outlier: 3.527A pdb=" N GLN A 658 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 718 removed outlier: 3.512A pdb=" N SER A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 736 through 745 removed outlier: 3.513A pdb=" N ILE A 740 " --> pdb=" O SER A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 779 Processing helix chain 'A' and resid 791 through 802 Processing helix chain 'A' and resid 803 through 806 Processing helix chain 'A' and resid 814 through 828 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 21 through 44 removed outlier: 3.751A pdb=" N SER B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.902A pdb=" N ASN B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.542A pdb=" N ILE B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.661A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 275 removed outlier: 3.806A pdb=" N ARG B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.922A pdb=" N GLN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 305 through 325 removed outlier: 3.903A pdb=" N LYS B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 343 through 369 removed outlier: 3.523A pdb=" N ALA B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.766A pdb=" N LEU B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 383' Processing helix chain 'B' and resid 387 through 399 Processing helix chain 'B' and resid 416 through 424 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.510A pdb=" N TRP B 448 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.026A pdb=" N VAL B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 508 through 513 removed outlier: 3.994A pdb=" N TYR B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 544 Processing helix chain 'B' and resid 588 through 597 Processing helix chain 'B' and resid 601 through 608 Processing helix chain 'B' and resid 617 through 622 Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.539A pdb=" N LEU B 631 " --> pdb=" O PRO B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 646 removed outlier: 4.005A pdb=" N ILE B 645 " --> pdb=" O PRO B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 653 removed outlier: 3.742A pdb=" N ILE B 653 " --> pdb=" O ALA B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.576A pdb=" N SER B 668 " --> pdb=" O ASN B 664 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 685 Processing helix chain 'B' and resid 703 through 709 removed outlier: 4.320A pdb=" N GLY B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 764 through 768 removed outlier: 3.875A pdb=" N GLU B 768 " --> pdb=" O GLY B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 Processing helix chain 'B' and resid 909 through 913 removed outlier: 3.538A pdb=" N LEU B 913 " --> pdb=" O PRO B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 935 removed outlier: 4.320A pdb=" N ILE B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 959 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1028 through 1039 Processing helix chain 'B' and resid 1040 through 1049 Processing helix chain 'B' and resid 1094 through 1106 removed outlier: 3.536A pdb=" N MET B1106 " --> pdb=" O GLU B1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 22 through 34 Processing helix chain 'C' and resid 42 through 59 Processing helix chain 'C' and resid 67 through 78 Processing helix chain 'C' and resid 79 through 82 Processing helix chain 'C' and resid 100 through 110 removed outlier: 3.753A pdb=" N ARG C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 4.378A pdb=" N THR C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 214 through 226 Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.574A pdb=" N ASN C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 283 through 301 Processing helix chain 'C' and resid 307 through 318 removed outlier: 3.971A pdb=" N ILE C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.514A pdb=" N ILE C 383 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.917A pdb=" N ILE D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 64 Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.863A pdb=" N HIS D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.265A pdb=" N CYS D 82 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.519A pdb=" N LEU D 114 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.751A pdb=" N GLU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.616A pdb=" N LYS D 211 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 212 " --> pdb=" O CYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 262 removed outlier: 3.592A pdb=" N LEU D 242 " --> pdb=" O PRO D 238 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 21 through 35 removed outlier: 3.516A pdb=" N ILE E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 4.119A pdb=" N ILE E 113 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.557A pdb=" N ILE E 126 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.706A pdb=" N SER E 182 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 30 removed outlier: 4.697A pdb=" N THR F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 46 removed outlier: 4.176A pdb=" N SER F 44 " --> pdb=" O ASP F 40 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE F 45 " --> pdb=" O TYR F 41 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 60 removed outlier: 3.563A pdb=" N LEU F 60 " --> pdb=" O ILE F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 77 removed outlier: 3.588A pdb=" N ARG F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.638A pdb=" N GLU F 106 " --> pdb=" O GLN F 102 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 36 Processing helix chain 'H' and resid 38 through 42 Processing helix chain 'H' and resid 49 through 56 removed outlier: 3.545A pdb=" N SER H 54 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE H 55 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 14 Processing helix chain 'K' and resid 19 through 35 Processing helix chain 'K' and resid 51 through 62 Processing helix chain 'L' and resid 21 through 33 removed outlier: 3.777A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 88 removed outlier: 3.555A pdb=" N LYS L 88 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 16 No H-bonds generated for 'chain 'N' and resid 14 through 16' Processing helix chain 'N' and resid 17 through 26 Processing helix chain 'N' and resid 30 through 39 Processing helix chain 'N' and resid 42 through 51 removed outlier: 3.704A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU N 49 " --> pdb=" O CYS N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'Q' and resid 37 through 58 Processing helix chain 'Q' and resid 62 through 77 Processing sheet with id=AA1, first strand: chain 'B' and resid 1111 through 1116 removed outlier: 6.157A pdb=" N GLY B1115 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE A 6 " --> pdb=" O GLY B1115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 82 removed outlier: 6.163A pdb=" N THR A 210 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N LYS A 79 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 10.135A pdb=" N ILE A 208 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.930A pdb=" N VAL A 173 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 318 removed outlier: 3.806A pdb=" N LEU B1025 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1001 through 1003 removed outlier: 7.726A pdb=" N PHE A 443 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 325 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 445 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER A 327 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.752A pdb=" N TYR A 377 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N HIS A 410 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA A 375 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 488 removed outlier: 4.504A pdb=" N GLY A 493 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 516 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.100A pdb=" N CYS G 69 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP G 114 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY G 7 " --> pdb=" O PHE G 54 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS G 26 " --> pdb=" O SER G 12 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE G 14 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL G 24 " --> pdb=" O ILE G 14 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE G 95 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU G 94 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU G 76 " --> pdb=" O GLU G 88 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER G 90 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU G 74 " --> pdb=" O SER G 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.386A pdb=" N VAL A 587 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 749 Processing sheet with id=AB3, first strand: chain 'A' and resid 830 through 832 removed outlier: 6.817A pdb=" N VAL A 838 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 47 removed outlier: 5.991A pdb=" N SER B 97 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 60 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE B 95 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR B 62 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER B 92 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP B 116 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 94 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB6, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AB7, first strand: chain 'B' and resid 339 through 342 removed outlier: 3.548A pdb=" N ALA B 161 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 171 through 174 removed outlier: 3.564A pdb=" N HIS B 183 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC1, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AC2, first strand: chain 'B' and resid 523 through 528 removed outlier: 6.714A pdb=" N VAL B 518 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR B 527 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER B 516 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.730A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.730A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL B 848 " --> pdb=" O MET P 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 702 Processing sheet with id=AC6, first strand: chain 'B' and resid 966 through 967 removed outlier: 7.338A pdb=" N ILE B 736 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 889 " --> pdb=" O ILE B 736 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N MET B 738 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ILE B 906 " --> pdb=" O ASN B 719 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 721 " --> pdb=" O ILE B 906 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 908 " --> pdb=" O ILE B 721 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA B 723 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 983 " --> pdb=" O ILE B 724 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 771 through 772 Processing sheet with id=AC8, first strand: chain 'B' and resid 807 through 809 removed outlier: 7.132A pdb=" N ILE B 835 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 897 through 898 Processing sheet with id=AD1, first strand: chain 'B' and resid 1054 through 1060 Processing sheet with id=AD2, first strand: chain 'B' and resid 1068 through 1069 Processing sheet with id=AD3, first strand: chain 'C' and resid 271 through 272 removed outlier: 3.510A pdb=" N MET C 120 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA Y 49 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 240 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.840A pdb=" N THR C 145 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 196 through 200 removed outlier: 6.307A pdb=" N SER C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 204 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 57 through 59 removed outlier: 4.550A pdb=" N LEU C 386 " --> pdb=" O ILE E 59 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.910A pdb=" N ARG D 14 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG D 8 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 11.145A pdb=" N SER D 221 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N THR D 171 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N GLU D 223 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 11.249A pdb=" N LYS D 169 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS D 225 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR D 167 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL D 161 " --> pdb=" O GLU D 231 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 115 through 116 removed outlier: 6.857A pdb=" N LYS D 138 " --> pdb=" O ASN D 49 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN D 49 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER D 140 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU D 43 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG D 146 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL D 41 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY D 148 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N MET D 39 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 107 through 109 removed outlier: 3.535A pdb=" N VAL D 131 " --> pdb=" O ILE D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 188 through 190 Processing sheet with id=AE2, first strand: chain 'E' and resid 2 through 4 removed outlier: 3.926A pdb=" N PHE E 2 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS F 11 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 48 through 53 removed outlier: 4.241A pdb=" N ASN E 50 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AE5, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.859A pdb=" N GLY E 169 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE E 146 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR E 162 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER E 148 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP E 105 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N LEU E 161 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU E 107 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR E 98 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU E 88 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 118 through 119 removed outlier: 4.115A pdb=" N LEU E 127 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 136 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.498A pdb=" N ILE H 45 " --> pdb=" O ILE H 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 2 through 8 removed outlier: 6.622A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU L 8 " --> pdb=" O TYR L 12 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 12 through 14 removed outlier: 3.548A pdb=" N LYS Y 12 " --> pdb=" O VAL Y 19 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 53 through 55 removed outlier: 6.893A pdb=" N VAL Y 58 " --> pdb=" O ILE Y 54 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU Y 73 " --> pdb=" O ARG Y 82 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG Y 82 " --> pdb=" O LEU Y 73 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.80: 28436 1.80 - 2.41: 56 2.41 - 3.03: 0 3.03 - 3.64: 0 3.64 - 4.25: 3 Bond restraints: 28495 Sorted by residual: bond pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.258 4.228 -1.970 2.00e-02 2.50e+03 9.70e+03 bond pdb=" S4 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.233 4.183 -1.950 2.00e-02 2.50e+03 9.51e+03 bond pdb=" S2 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 2.300 4.249 -1.949 2.00e-02 2.50e+03 9.49e+03 bond pdb=" S2 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.317 2.205 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.296 2.194 0.102 2.00e-02 2.50e+03 2.62e+01 ... (remaining 28490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.98: 38443 14.98 - 29.96: 12 29.96 - 44.95: 1 44.95 - 59.93: 0 59.93 - 74.91: 2 Bond angle restraints: 38458 Sorted by residual: angle pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " pdb=" S3 F3S D 301 " ideal model delta sigma weight residual 114.75 39.84 74.91 3.00e+00 1.11e-01 6.23e+02 angle pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.59 41.42 71.17 3.00e+00 1.11e-01 5.63e+02 angle pdb=" S1 F3S D 301 " pdb="FE3 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.54 146.12 -33.58 3.00e+00 1.11e-01 1.25e+02 angle pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 74.86 45.08 29.78 3.00e+00 1.11e-01 9.86e+01 angle pdb=" S2 F3S D 301 " pdb="FE3 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 103.26 74.40 28.86 3.00e+00 1.11e-01 9.26e+01 ... (remaining 38453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 15841 17.57 - 35.14: 1455 35.14 - 52.70: 213 52.70 - 70.27: 54 70.27 - 87.84: 19 Dihedral angle restraints: 17582 sinusoidal: 7338 harmonic: 10244 Sorted by residual: dihedral pdb=" CA VAL B1080 " pdb=" C VAL B1080 " pdb=" N HIS B1081 " pdb=" CA HIS B1081 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PHE B 212 " pdb=" C PHE B 212 " pdb=" N ALA B 213 " pdb=" CA ALA B 213 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE C 206 " pdb=" C ILE C 206 " pdb=" N TYR C 207 " pdb=" CA TYR C 207 " ideal model delta harmonic sigma weight residual 180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 17579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.548: 4382 2.548 - 5.095: 0 5.095 - 7.643: 0 7.643 - 10.191: 0 10.191 - 12.738: 1 Chirality restraints: 4383 Sorted by residual: chirality pdb=" S2 F3S D 301 " pdb="FE1 F3S D 301 " pdb="FE3 F3S D 301 " pdb="FE4 F3S D 301 " both_signs ideal model delta sigma weight residual False 10.77 -1.97 12.74 2.00e-01 2.50e+01 4.06e+03 chirality pdb=" CB ILE Y 92 " pdb=" CA ILE Y 92 " pdb=" CG1 ILE Y 92 " pdb=" CG2 ILE Y 92 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE C 21 " pdb=" N ILE C 21 " pdb=" C ILE C 21 " pdb=" CB ILE C 21 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 4380 not shown) Planarity restraints: 4927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B1081 " 0.035 2.00e-02 2.50e+03 4.05e-02 2.46e+01 pdb=" CG HIS B1081 " -0.087 2.00e-02 2.50e+03 pdb=" ND1 HIS B1081 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS B1081 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS B1081 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B1081 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 33 " -0.013 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C ILE C 33 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE C 33 " -0.018 2.00e-02 2.50e+03 pdb=" N MET C 34 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 302 " -0.031 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO B 303 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 303 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 303 " -0.027 5.00e-02 4.00e+02 ... (remaining 4924 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 81 2.45 - 3.07: 16995 3.07 - 3.68: 39782 3.68 - 4.29: 63303 4.29 - 4.90: 107437 Nonbonded interactions: 227598 Sorted by model distance: nonbonded pdb=" OD1 ASP A 458 " pdb=" OD1 ASP A 460 " model vdw 1.842 3.040 nonbonded pdb=" CG HIS B1081 " pdb="ZN ZN B1201 " model vdw 1.928 1.960 nonbonded pdb=" O ARG A 573 " pdb="ZN ZN A 904 " model vdw 2.002 2.230 nonbonded pdb=" OD1 ASP A 458 " pdb="MG MG A 901 " model vdw 2.018 2.170 nonbonded pdb=" OE2 GLU P 12 " pdb="ZN ZN P 101 " model vdw 2.021 2.230 ... (remaining 227593 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=0.50 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: 2.350 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.810 Find NCS groups from input model: 0.140 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.020 1.970 28527 Z= 1.013 Angle : 0.935 74.909 38494 Z= 0.366 Chirality : 0.198 12.738 4383 Planarity : 0.004 0.048 4927 Dihedral : 13.679 87.837 10992 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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 (0.14), residues: 3497 helix: 0.54 (0.16), residues: 1198 sheet: -0.10 (0.21), residues: 592 loop : -0.74 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.015 0.001 TYR A 91 PHE 0.014 0.001 PHE A 419 TRP 0.015 0.001 TRP B 8 HIS 0.048 0.001 HIS B1081 Details of bonding type rmsd covalent geometry : bond 0.02029 (28495) covalent geometry : angle 0.87524 (38458) hydrogen bonds : bond 0.19282 ( 1170) hydrogen bonds : angle 6.81053 ( 3270) metal coordination : bond 0.01081 ( 32) metal coordination : angle 10.81849 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.7931 (ptt) cc_final: 0.7651 (ptt) REVERT: A 131 ARG cc_start: 0.6916 (mtm180) cc_final: 0.6647 (mtt90) REVERT: A 200 LYS cc_start: 0.8380 (ptpp) cc_final: 0.8114 (pttm) REVERT: A 267 ASP cc_start: 0.7413 (m-30) cc_final: 0.6919 (t0) REVERT: A 363 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8449 (mm-40) REVERT: A 458 ASP cc_start: 0.6273 (p0) cc_final: 0.5958 (p0) REVERT: A 646 MET cc_start: 0.8689 (ttt) cc_final: 0.8452 (ttt) REVERT: B 346 ASP cc_start: 0.7337 (m-30) cc_final: 0.7023 (m-30) REVERT: B 770 LYS cc_start: 0.8240 (mttp) cc_final: 0.8036 (mttm) REVERT: B 891 ASP cc_start: 0.7135 (m-30) cc_final: 0.6829 (m-30) REVERT: B 995 MET cc_start: 0.9012 (mtm) cc_final: 0.8783 (mtt) REVERT: C 34 MET cc_start: 0.8733 (mmt) cc_final: 0.8445 (mmt) REVERT: C 133 ASP cc_start: 0.6507 (m-30) cc_final: 0.6281 (m-30) REVERT: C 187 THR cc_start: 0.8125 (m) cc_final: 0.7871 (m) REVERT: C 246 GLU cc_start: 0.7869 (tt0) cc_final: 0.7585 (tt0) REVERT: D 18 GLU cc_start: 0.7995 (tt0) cc_final: 0.7787 (tt0) REVERT: E 163 MET cc_start: -0.1294 (mmp) cc_final: -0.1841 (tpp) REVERT: G 10 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7650 (ttmm) REVERT: G 15 GLU cc_start: 0.7392 (mp0) cc_final: 0.7155 (mp0) REVERT: G 50 GLU cc_start: 0.8468 (pt0) cc_final: 0.8115 (pt0) REVERT: N 19 GLU cc_start: 0.6864 (mp0) cc_final: 0.6546 (mp0) REVERT: Q 45 MET cc_start: 0.7770 (ttp) cc_final: 0.7328 (ttp) REVERT: Q 49 ASP cc_start: 0.7156 (m-30) cc_final: 0.6564 (m-30) REVERT: Y 77 LYS cc_start: 0.6708 (ptmt) cc_final: 0.6505 (ttpt) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.8198 time to fit residues: 440.4107 Evaluate side-chains 413 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN A 606 GLN B 197 GLN B 245 GLN B 400 ASN B 582 ASN B1001 HIS C 199 ASN C 271 GLN C 326 GLN C 375 GLN D 75 HIS D 94 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.171666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109593 restraints weight = 26332.211| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.04 r_work: 0.3054 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.191 28527 Z= 0.143 Angle : 1.014 65.436 38494 Z= 0.339 Chirality : 0.050 1.423 4383 Planarity : 0.004 0.046 4927 Dihedral : 4.407 59.584 3884 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.16 % Allowed : 7.65 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: -0.06 (0.14), residues: 3497 helix: 0.81 (0.15), residues: 1225 sheet: 0.02 (0.21), residues: 595 loop : -0.63 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 79 TYR 0.015 0.001 TYR B 294 PHE 0.013 0.001 PHE A 419 TRP 0.011 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00307 (28495) covalent geometry : angle 0.77587 (38458) hydrogen bonds : bond 0.04556 ( 1170) hydrogen bonds : angle 4.96608 ( 3270) metal coordination : bond 0.00669 ( 32) metal coordination : angle 21.37771 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 454 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.7036 (mtm180) cc_final: 0.6661 (mtt90) REVERT: A 200 LYS cc_start: 0.8431 (ptpp) cc_final: 0.8132 (pttm) REVERT: A 202 SER cc_start: 0.8492 (t) cc_final: 0.8287 (m) REVERT: A 267 ASP cc_start: 0.7455 (m-30) cc_final: 0.6872 (t0) REVERT: A 346 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8566 (ttm) REVERT: A 622 GLU cc_start: 0.7188 (pm20) cc_final: 0.6982 (pm20) REVERT: A 737 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7000 (tt0) REVERT: B 171 LEU cc_start: 0.8219 (mt) cc_final: 0.7975 (mt) REVERT: B 197 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: B 594 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7411 (mttp) REVERT: B 599 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: B 838 ARG cc_start: 0.8466 (mtt-85) cc_final: 0.8040 (mtm180) REVERT: B 891 ASP cc_start: 0.8116 (m-30) cc_final: 0.7831 (m-30) REVERT: B 995 MET cc_start: 0.8988 (mtm) cc_final: 0.8782 (mtt) REVERT: C 35 ASP cc_start: 0.7887 (m-30) cc_final: 0.7553 (m-30) REVERT: C 44 GLU cc_start: 0.7389 (tt0) cc_final: 0.6784 (mp0) REVERT: C 203 SER cc_start: 0.7485 (OUTLIER) cc_final: 0.7166 (t) REVERT: C 246 GLU cc_start: 0.7891 (tt0) cc_final: 0.7631 (tt0) REVERT: C 351 HIS cc_start: 0.7692 (m-70) cc_final: 0.7430 (m170) REVERT: D 71 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: E 163 MET cc_start: -0.1204 (mmp) cc_final: -0.1672 (tpp) REVERT: G 15 GLU cc_start: 0.7713 (mp0) cc_final: 0.7341 (mp0) REVERT: G 39 ILE cc_start: 0.8688 (pt) cc_final: 0.8470 (pt) REVERT: G 50 GLU cc_start: 0.8519 (pt0) cc_final: 0.8054 (pt0) REVERT: H 67 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7780 (mtm180) REVERT: K 1 MET cc_start: 0.5194 (ttt) cc_final: 0.4954 (ttm) REVERT: K 11 LYS cc_start: 0.8763 (mtmp) cc_final: 0.8561 (mtpt) REVERT: L 21 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7442 (pp20) REVERT: L 86 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8054 (mt-10) REVERT: N 19 GLU cc_start: 0.7197 (mp0) cc_final: 0.6687 (mp0) REVERT: P 12 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: P 16 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8220 (p0) REVERT: Q 45 MET cc_start: 0.7471 (ttp) cc_final: 0.7136 (ttp) REVERT: Q 49 ASP cc_start: 0.7264 (m-30) cc_final: 0.6805 (m-30) REVERT: Y 12 LYS cc_start: 0.7024 (ptpp) cc_final: 0.6823 (ptpp) REVERT: Y 77 LYS cc_start: 0.6783 (ptmt) cc_final: 0.6468 (ttpt) outliers start: 36 outliers final: 11 residues processed: 467 average time/residue: 0.8487 time to fit residues: 447.7947 Evaluate side-chains 442 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 421 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 143 optimal weight: 6.9990 chunk 334 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 254 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 333 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 327 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN B 197 GLN B 245 GLN B 400 ASN B 582 ASN B 667 GLN B1001 HIS C 271 GLN C 375 GLN D 75 HIS D 94 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.170397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109489 restraints weight = 25975.439| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.28 r_work: 0.2992 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 28527 Z= 0.211 Angle : 0.946 67.609 38494 Z= 0.362 Chirality : 0.053 1.464 4383 Planarity : 0.005 0.052 4927 Dihedral : 4.729 63.818 3884 Min Nonbonded Distance : 1.524 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.97 % Allowed : 9.65 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: -0.18 (0.14), residues: 3497 helix: 0.75 (0.15), residues: 1223 sheet: -0.06 (0.21), residues: 596 loop : -0.73 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 79 TYR 0.023 0.002 TYR A 850 PHE 0.017 0.002 PHE B 359 TRP 0.012 0.002 TRP A 372 HIS 0.013 0.002 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00509 (28495) covalent geometry : angle 0.80081 (38458) hydrogen bonds : bond 0.05335 ( 1170) hydrogen bonds : angle 4.86968 ( 3270) metal coordination : bond 0.00661 ( 32) metal coordination : angle 16.47890 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 433 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8470 (ptpp) cc_final: 0.8223 (pttm) REVERT: A 267 ASP cc_start: 0.7475 (m-30) cc_final: 0.6892 (t0) REVERT: A 346 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8761 (ttp) REVERT: A 622 GLU cc_start: 0.7347 (pm20) cc_final: 0.7144 (pm20) REVERT: A 737 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7159 (tt0) REVERT: B 590 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6549 (mm-30) REVERT: B 593 LYS cc_start: 0.7574 (mttp) cc_final: 0.7281 (mtmm) REVERT: B 597 ASN cc_start: 0.7454 (m110) cc_final: 0.7174 (m-40) REVERT: B 770 LYS cc_start: 0.8499 (mttp) cc_final: 0.8257 (mttm) REVERT: B 835 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7606 (pt) REVERT: B 838 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8103 (mtm180) REVERT: B 891 ASP cc_start: 0.8158 (m-30) cc_final: 0.7825 (m-30) REVERT: B 995 MET cc_start: 0.9122 (mtm) cc_final: 0.8765 (mtt) REVERT: C 35 ASP cc_start: 0.8048 (m-30) cc_final: 0.7641 (m-30) REVERT: C 44 GLU cc_start: 0.7430 (tt0) cc_final: 0.6814 (mp0) REVERT: C 82 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: C 133 ASP cc_start: 0.6698 (m-30) cc_final: 0.6460 (m-30) REVERT: C 203 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7220 (t) REVERT: C 351 HIS cc_start: 0.7783 (m-70) cc_final: 0.7509 (m170) REVERT: D 71 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: E 145 MET cc_start: 0.2617 (tmt) cc_final: 0.2179 (tmt) REVERT: E 163 MET cc_start: -0.0492 (mmp) cc_final: -0.0986 (tpp) REVERT: G 15 GLU cc_start: 0.7776 (mp0) cc_final: 0.7410 (mp0) REVERT: G 50 GLU cc_start: 0.8570 (pt0) cc_final: 0.8029 (pt0) REVERT: G 77 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: G 99 LEU cc_start: 0.7824 (mm) cc_final: 0.7574 (mm) REVERT: H 67 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7775 (mtm180) REVERT: K 1 MET cc_start: 0.5075 (ttt) cc_final: 0.4852 (ttm) REVERT: K 11 LYS cc_start: 0.8858 (mtmp) cc_final: 0.8632 (mtpt) REVERT: L 21 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: L 86 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8191 (mt-10) REVERT: N 19 GLU cc_start: 0.7269 (mp0) cc_final: 0.6749 (mp0) REVERT: P 16 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8185 (p0) REVERT: Q 45 MET cc_start: 0.7465 (ttp) cc_final: 0.6881 (ttp) REVERT: Q 49 ASP cc_start: 0.7302 (m-30) cc_final: 0.6842 (m-30) REVERT: Y 77 LYS cc_start: 0.6912 (ptmt) cc_final: 0.6570 (ttpt) outliers start: 61 outliers final: 29 residues processed: 462 average time/residue: 0.8399 time to fit residues: 439.5170 Evaluate side-chains 457 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 418 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 61 LYS Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 264 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 206 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 329 optimal weight: 0.9980 chunk 280 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN B 197 GLN B 400 ASN B 582 ASN B1001 HIS ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 375 GLN D 75 HIS D 94 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110455 restraints weight = 25959.420| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.30 r_work: 0.3004 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 28527 Z= 0.167 Angle : 0.936 85.897 38494 Z= 0.337 Chirality : 0.051 1.289 4383 Planarity : 0.005 0.048 4927 Dihedral : 4.677 61.728 3884 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.13 % Allowed : 11.42 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: -0.12 (0.14), residues: 3497 helix: 0.82 (0.15), residues: 1225 sheet: -0.07 (0.21), residues: 604 loop : -0.70 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 68 TYR 0.020 0.001 TYR A 850 PHE 0.017 0.002 PHE B 359 TRP 0.012 0.001 TRP B 8 HIS 0.021 0.001 HIS B1081 Details of bonding type rmsd covalent geometry : bond 0.00400 (28495) covalent geometry : angle 0.73257 (38458) hydrogen bonds : bond 0.04780 ( 1170) hydrogen bonds : angle 4.74827 ( 3270) metal coordination : bond 0.03837 ( 32) metal coordination : angle 19.05802 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 434 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8473 (ptpp) cc_final: 0.8246 (pttm) REVERT: A 267 ASP cc_start: 0.7413 (m-30) cc_final: 0.6823 (t0) REVERT: A 346 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8697 (ttp) REVERT: A 622 GLU cc_start: 0.7253 (pm20) cc_final: 0.7031 (pm20) REVERT: A 737 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7054 (tt0) REVERT: B 61 ARG cc_start: 0.8321 (ptt90) cc_final: 0.8106 (ptt90) REVERT: B 171 LEU cc_start: 0.8309 (mt) cc_final: 0.8062 (mt) REVERT: B 255 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6899 (tt0) REVERT: B 590 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6448 (mm-30) REVERT: B 617 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: B 759 GLU cc_start: 0.8157 (tt0) cc_final: 0.7939 (tt0) REVERT: B 770 LYS cc_start: 0.8445 (mttp) cc_final: 0.8196 (mttm) REVERT: B 835 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7513 (pt) REVERT: B 891 ASP cc_start: 0.8162 (m-30) cc_final: 0.7855 (m-30) REVERT: B 995 MET cc_start: 0.9136 (mtm) cc_final: 0.8852 (mtt) REVERT: C 35 ASP cc_start: 0.7958 (m-30) cc_final: 0.7492 (m-30) REVERT: C 44 GLU cc_start: 0.7365 (tt0) cc_final: 0.6743 (mp0) REVERT: C 203 SER cc_start: 0.7535 (OUTLIER) cc_final: 0.7185 (t) REVERT: D 71 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: D 223 GLU cc_start: 0.7733 (pm20) cc_final: 0.7250 (mp0) REVERT: E 69 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7165 (mm-30) REVERT: E 145 MET cc_start: 0.2605 (tmt) cc_final: 0.2114 (tmt) REVERT: E 163 MET cc_start: -0.0285 (mmp) cc_final: -0.0748 (tpp) REVERT: G 15 GLU cc_start: 0.7776 (mp0) cc_final: 0.7391 (mp0) REVERT: G 50 GLU cc_start: 0.8558 (pt0) cc_final: 0.7993 (pt0) REVERT: G 77 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8572 (tt0) REVERT: G 99 LEU cc_start: 0.7770 (mm) cc_final: 0.7522 (mm) REVERT: H 67 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7857 (mtm180) REVERT: K 11 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8559 (mtpt) REVERT: L 21 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7259 (pp20) REVERT: L 86 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8123 (mt-10) REVERT: N 19 GLU cc_start: 0.7224 (mp0) cc_final: 0.6680 (mp0) REVERT: P 12 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: P 16 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8150 (p0) REVERT: Q 45 MET cc_start: 0.7323 (ttp) cc_final: 0.6667 (ttp) REVERT: Q 49 ASP cc_start: 0.7239 (m-30) cc_final: 0.6781 (m-30) REVERT: Y 12 LYS cc_start: 0.6885 (ptpp) cc_final: 0.6671 (ptpp) REVERT: Y 77 LYS cc_start: 0.6894 (ptmt) cc_final: 0.6541 (ttpt) outliers start: 66 outliers final: 38 residues processed: 466 average time/residue: 0.8096 time to fit residues: 428.2473 Evaluate side-chains 471 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 421 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 61 LYS Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 221 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 308 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 255 optimal weight: 0.1980 chunk 129 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN B 400 ASN B1001 HIS ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN C 271 GLN C 375 GLN D 75 HIS D 94 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112645 restraints weight = 25967.866| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.32 r_work: 0.3042 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 28527 Z= 0.118 Angle : 0.884 84.007 38494 Z= 0.309 Chirality : 0.050 1.438 4383 Planarity : 0.004 0.048 4927 Dihedral : 4.402 58.957 3884 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.94 % Allowed : 12.39 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.09 (0.14), residues: 3497 helix: 1.04 (0.15), residues: 1225 sheet: 0.03 (0.21), residues: 594 loop : -0.60 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 68 TYR 0.014 0.001 TYR N 43 PHE 0.014 0.001 PHE B 359 TRP 0.011 0.001 TRP B 8 HIS 0.016 0.001 HIS B1081 Details of bonding type rmsd covalent geometry : bond 0.00266 (28495) covalent geometry : angle 0.68313 (38458) hydrogen bonds : bond 0.03880 ( 1170) hydrogen bonds : angle 4.54123 ( 3270) metal coordination : bond 0.02713 ( 32) metal coordination : angle 18.38322 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 437 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8226 (pttm) REVERT: A 267 ASP cc_start: 0.7293 (m-30) cc_final: 0.6716 (t0) REVERT: A 346 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8655 (ttp) REVERT: A 737 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7013 (tt0) REVERT: B 171 LEU cc_start: 0.8177 (mt) cc_final: 0.7931 (mt) REVERT: B 255 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6981 (tt0) REVERT: B 540 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 759 GLU cc_start: 0.8111 (tt0) cc_final: 0.7904 (tt0) REVERT: B 770 LYS cc_start: 0.8386 (mttp) cc_final: 0.8118 (mttm) REVERT: B 835 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7457 (pt) REVERT: B 891 ASP cc_start: 0.8142 (m-30) cc_final: 0.7865 (m-30) REVERT: C 35 ASP cc_start: 0.7924 (m-30) cc_final: 0.7378 (m-30) REVERT: C 44 GLU cc_start: 0.7357 (tt0) cc_final: 0.6740 (mp0) REVERT: C 181 GLU cc_start: 0.6883 (pt0) cc_final: 0.6348 (pt0) REVERT: C 203 SER cc_start: 0.7536 (OUTLIER) cc_final: 0.7102 (t) REVERT: C 222 GLU cc_start: 0.6735 (pt0) cc_final: 0.6506 (mp0) REVERT: D 71 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: D 223 GLU cc_start: 0.7715 (pm20) cc_final: 0.7250 (mp0) REVERT: E 69 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7145 (mm-30) REVERT: E 145 MET cc_start: 0.2712 (tmt) cc_final: 0.2360 (tmt) REVERT: E 163 MET cc_start: -0.0183 (mmp) cc_final: -0.0637 (tpp) REVERT: G 15 GLU cc_start: 0.7690 (mp0) cc_final: 0.7278 (mp0) REVERT: G 77 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: G 99 LEU cc_start: 0.7744 (mm) cc_final: 0.7456 (mm) REVERT: K 11 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8485 (mtpt) REVERT: L 21 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7410 (pp20) REVERT: L 86 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8021 (mt-10) REVERT: N 19 GLU cc_start: 0.7209 (mp0) cc_final: 0.6675 (mp0) REVERT: P 16 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8055 (p0) REVERT: Q 45 MET cc_start: 0.7209 (ttp) cc_final: 0.6730 (ttp) REVERT: Q 49 ASP cc_start: 0.7207 (m-30) cc_final: 0.6769 (m-30) REVERT: Y 77 LYS cc_start: 0.6892 (ptmt) cc_final: 0.6537 (ttpt) outliers start: 60 outliers final: 30 residues processed: 467 average time/residue: 0.8064 time to fit residues: 427.7930 Evaluate side-chains 460 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 422 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 958 LYS Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 61 LYS Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 327 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN B1001 HIS ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN D 75 HIS D 94 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109996 restraints weight = 25864.332| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.32 r_work: 0.3000 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 28527 Z= 0.185 Angle : 0.943 83.759 38494 Z= 0.340 Chirality : 0.052 1.470 4383 Planarity : 0.005 0.049 4927 Dihedral : 4.639 62.962 3884 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.03 % Allowed : 13.33 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: -0.03 (0.14), residues: 3497 helix: 0.93 (0.15), residues: 1223 sheet: -0.03 (0.21), residues: 594 loop : -0.67 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 68 TYR 0.022 0.002 TYR A 850 PHE 0.017 0.002 PHE B 359 TRP 0.012 0.002 TRP B 8 HIS 0.015 0.002 HIS B1081 Details of bonding type rmsd covalent geometry : bond 0.00451 (28495) covalent geometry : angle 0.73759 (38458) hydrogen bonds : bond 0.04816 ( 1170) hydrogen bonds : angle 4.62503 ( 3270) metal coordination : bond 0.03164 ( 32) metal coordination : angle 19.25222 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 427 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8464 (ptpp) cc_final: 0.8233 (pttm) REVERT: A 267 ASP cc_start: 0.7403 (m-30) cc_final: 0.6816 (t0) REVERT: A 346 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8707 (ttp) REVERT: A 737 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7102 (tt0) REVERT: B 61 ARG cc_start: 0.8385 (ptt90) cc_final: 0.7932 (ptt90) REVERT: B 68 ARG cc_start: 0.7227 (ttm-80) cc_final: 0.6989 (ttm170) REVERT: B 171 LEU cc_start: 0.8242 (mt) cc_final: 0.7985 (mt) REVERT: B 245 GLN cc_start: 0.8288 (tt0) cc_final: 0.8069 (tt0) REVERT: B 255 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6994 (tt0) REVERT: B 540 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7386 (mm-30) REVERT: B 590 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: B 594 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7421 (mttp) REVERT: B 759 GLU cc_start: 0.8186 (tt0) cc_final: 0.7971 (tt0) REVERT: B 770 LYS cc_start: 0.8436 (mttp) cc_final: 0.8125 (mttm) REVERT: B 835 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7594 (pt) REVERT: B 1104 MET cc_start: 0.8042 (mtm) cc_final: 0.7816 (mtp) REVERT: C 35 ASP cc_start: 0.7943 (m-30) cc_final: 0.7395 (m-30) REVERT: C 44 GLU cc_start: 0.7380 (tt0) cc_final: 0.6744 (mp0) REVERT: C 82 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8432 (mt0) REVERT: C 181 GLU cc_start: 0.7048 (pt0) cc_final: 0.6511 (pt0) REVERT: C 200 ASP cc_start: 0.7149 (t70) cc_final: 0.6794 (t0) REVERT: C 203 SER cc_start: 0.7528 (OUTLIER) cc_final: 0.7158 (t) REVERT: D 71 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: E 145 MET cc_start: 0.2528 (OUTLIER) cc_final: 0.2166 (tmt) REVERT: E 163 MET cc_start: -0.0456 (mmp) cc_final: -0.0947 (tpp) REVERT: G 15 GLU cc_start: 0.7787 (mp0) cc_final: 0.7393 (mp0) REVERT: G 50 GLU cc_start: 0.8556 (pt0) cc_final: 0.8091 (pt0) REVERT: G 77 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: G 99 LEU cc_start: 0.7789 (mm) cc_final: 0.7525 (mm) REVERT: K 11 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8551 (mtpt) REVERT: K 15 LYS cc_start: 0.7758 (tppt) cc_final: 0.7452 (ttmt) REVERT: L 21 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: L 86 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8090 (mt-10) REVERT: N 19 GLU cc_start: 0.7261 (mp0) cc_final: 0.6715 (mp0) REVERT: P 16 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8130 (p0) REVERT: Q 45 MET cc_start: 0.7291 (ttp) cc_final: 0.6676 (ttp) REVERT: Q 49 ASP cc_start: 0.7237 (m-30) cc_final: 0.6778 (m-30) REVERT: Y 12 LYS cc_start: 0.6901 (ptpp) cc_final: 0.6664 (ptpp) REVERT: Y 77 LYS cc_start: 0.6934 (ptmt) cc_final: 0.6569 (ttpt) outliers start: 63 outliers final: 35 residues processed: 457 average time/residue: 0.8369 time to fit residues: 434.2014 Evaluate side-chains 471 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 424 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 61 LYS Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 85 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 252 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN B1001 HIS C 271 GLN C 375 GLN D 75 HIS D 94 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN K 33 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112531 restraints weight = 25799.743| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.36 r_work: 0.3040 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 28527 Z= 0.116 Angle : 0.883 83.989 38494 Z= 0.308 Chirality : 0.049 1.446 4383 Planarity : 0.004 0.048 4927 Dihedral : 4.363 57.560 3884 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.90 % Allowed : 14.00 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.15 (0.14), residues: 3497 helix: 1.14 (0.15), residues: 1222 sheet: 0.04 (0.21), residues: 584 loop : -0.59 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 68 TYR 0.015 0.001 TYR C 128 PHE 0.014 0.001 PHE B 359 TRP 0.012 0.001 TRP B 8 HIS 0.015 0.001 HIS B1081 Details of bonding type rmsd covalent geometry : bond 0.00262 (28495) covalent geometry : angle 0.68317 (38458) hydrogen bonds : bond 0.03743 ( 1170) hydrogen bonds : angle 4.44830 ( 3270) metal coordination : bond 0.02754 ( 32) metal coordination : angle 18.30375 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 435 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8406 (ptpp) cc_final: 0.8195 (pttm) REVERT: A 267 ASP cc_start: 0.7279 (m-30) cc_final: 0.6697 (t0) REVERT: A 346 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8665 (ttp) REVERT: A 646 MET cc_start: 0.8976 (ttt) cc_final: 0.8768 (ttt) REVERT: A 737 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7002 (tt0) REVERT: B 61 ARG cc_start: 0.8314 (ptt90) cc_final: 0.7988 (ptt90) REVERT: B 68 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6864 (ttm170) REVERT: B 171 LEU cc_start: 0.8194 (mt) cc_final: 0.7940 (mt) REVERT: B 245 GLN cc_start: 0.8188 (tt0) cc_final: 0.7967 (tt0) REVERT: B 255 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6978 (tt0) REVERT: B 458 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: B 540 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 544 GLN cc_start: 0.8434 (mt0) cc_final: 0.7887 (mt0) REVERT: B 590 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6417 (mm-30) REVERT: B 594 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7428 (mttp) REVERT: B 759 GLU cc_start: 0.8118 (tt0) cc_final: 0.7912 (tt0) REVERT: B 835 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7466 (pt) REVERT: B 958 LYS cc_start: 0.8134 (mmpt) cc_final: 0.7649 (mttp) REVERT: C 35 ASP cc_start: 0.7972 (m-30) cc_final: 0.7417 (m-30) REVERT: C 181 GLU cc_start: 0.7043 (pt0) cc_final: 0.6502 (pt0) REVERT: C 200 ASP cc_start: 0.7301 (t70) cc_final: 0.6818 (t0) REVERT: C 203 SER cc_start: 0.7517 (OUTLIER) cc_final: 0.7115 (t) REVERT: D 71 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: D 223 GLU cc_start: 0.7687 (mp0) cc_final: 0.7374 (mp0) REVERT: E 69 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7162 (mm-30) REVERT: E 145 MET cc_start: 0.2486 (OUTLIER) cc_final: 0.2140 (tmt) REVERT: E 163 MET cc_start: -0.0389 (mmp) cc_final: -0.0809 (tpp) REVERT: G 5 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8206 (tpp) REVERT: G 15 GLU cc_start: 0.7717 (mp0) cc_final: 0.7323 (mp0) REVERT: G 50 GLU cc_start: 0.8577 (pt0) cc_final: 0.8050 (pt0) REVERT: G 77 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: G 99 LEU cc_start: 0.7717 (mm) cc_final: 0.7439 (mm) REVERT: K 11 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8474 (mtpt) REVERT: L 21 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: L 86 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8007 (mt-10) REVERT: N 19 GLU cc_start: 0.7203 (mp0) cc_final: 0.6673 (mp0) REVERT: Q 45 MET cc_start: 0.7068 (ttp) cc_final: 0.6518 (ttp) REVERT: Q 49 ASP cc_start: 0.7189 (m-30) cc_final: 0.6748 (m-30) REVERT: Y 12 LYS cc_start: 0.6918 (ptpp) cc_final: 0.6614 (ptpp) REVERT: Y 14 LYS cc_start: 0.6389 (ttmt) cc_final: 0.5985 (tttm) REVERT: Y 77 LYS cc_start: 0.6911 (ptmt) cc_final: 0.6548 (ttpt) outliers start: 59 outliers final: 35 residues processed: 463 average time/residue: 0.8014 time to fit residues: 421.7339 Evaluate side-chains 473 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 426 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 37 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN C 271 GLN D 75 HIS D 94 ASN D 192 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN K 33 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.105177 restraints weight = 26240.591| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.29 r_work: 0.2940 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 28527 Z= 0.156 Angle : 0.918 83.884 38494 Z= 0.326 Chirality : 0.051 1.458 4383 Planarity : 0.004 0.048 4927 Dihedral : 4.489 60.777 3884 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.97 % Allowed : 14.39 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.10 (0.14), residues: 3497 helix: 1.07 (0.15), residues: 1222 sheet: 0.10 (0.21), residues: 573 loop : -0.64 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 79 TYR 0.018 0.001 TYR A 850 PHE 0.016 0.002 PHE B 359 TRP 0.012 0.001 TRP B 8 HIS 0.013 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00376 (28495) covalent geometry : angle 0.71503 (38458) hydrogen bonds : bond 0.04332 ( 1170) hydrogen bonds : angle 4.50015 ( 3270) metal coordination : bond 0.02262 ( 32) metal coordination : angle 18.86465 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 429 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8177 (pttm) REVERT: A 267 ASP cc_start: 0.7338 (m-30) cc_final: 0.6740 (t0) REVERT: A 346 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8705 (ttp) REVERT: A 737 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7040 (tt0) REVERT: B 61 ARG cc_start: 0.8329 (ptt90) cc_final: 0.7988 (ptt90) REVERT: B 68 ARG cc_start: 0.7220 (ttm-80) cc_final: 0.6988 (ttm170) REVERT: B 171 LEU cc_start: 0.8227 (mt) cc_final: 0.7964 (mt) REVERT: B 245 GLN cc_start: 0.8185 (tt0) cc_final: 0.7969 (tt0) REVERT: B 255 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7005 (tt0) REVERT: B 458 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: B 540 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 544 GLN cc_start: 0.8454 (mt0) cc_final: 0.7992 (mt0) REVERT: B 590 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6421 (mm-30) REVERT: B 594 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7445 (mttp) REVERT: B 759 GLU cc_start: 0.8225 (tt0) cc_final: 0.7958 (tt0) REVERT: B 835 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7559 (pt) REVERT: B 891 ASP cc_start: 0.8183 (m-30) cc_final: 0.7932 (m-30) REVERT: C 35 ASP cc_start: 0.7989 (m-30) cc_final: 0.7438 (m-30) REVERT: C 44 GLU cc_start: 0.7424 (tt0) cc_final: 0.6765 (mp0) REVERT: C 181 GLU cc_start: 0.7026 (pt0) cc_final: 0.6509 (pt0) REVERT: C 200 ASP cc_start: 0.7350 (t70) cc_final: 0.6819 (t0) REVERT: C 203 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7082 (t) REVERT: D 71 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: E 163 MET cc_start: -0.0222 (mmp) cc_final: -0.0682 (tpp) REVERT: G 5 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8246 (tpp) REVERT: G 15 GLU cc_start: 0.7715 (mp0) cc_final: 0.7343 (mp0) REVERT: G 41 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7988 (mmpt) REVERT: G 42 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: G 50 GLU cc_start: 0.8596 (pt0) cc_final: 0.8110 (pt0) REVERT: G 77 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: G 99 LEU cc_start: 0.7781 (mm) cc_final: 0.7517 (mm) REVERT: K 11 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8514 (mtpt) REVERT: L 21 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7266 (pp20) REVERT: L 86 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8053 (mt-10) REVERT: N 19 GLU cc_start: 0.7238 (mp0) cc_final: 0.6705 (mp0) REVERT: P 16 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8097 (p0) REVERT: Q 45 MET cc_start: 0.7091 (ttp) cc_final: 0.6494 (ttp) REVERT: Q 49 ASP cc_start: 0.7229 (m-30) cc_final: 0.6786 (m-30) REVERT: Y 12 LYS cc_start: 0.6921 (ptpp) cc_final: 0.6643 (ptpp) REVERT: Y 14 LYS cc_start: 0.6461 (ttmt) cc_final: 0.6050 (tttm) REVERT: Y 77 LYS cc_start: 0.6930 (ptmt) cc_final: 0.6550 (ttpt) outliers start: 61 outliers final: 39 residues processed: 456 average time/residue: 0.8173 time to fit residues: 423.4165 Evaluate side-chains 477 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 424 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 61 LYS Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 240 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 319 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 334 optimal weight: 0.6980 chunk 342 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN B1001 HIS C 271 GLN C 375 GLN D 75 HIS D 94 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN K 33 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107117 restraints weight = 26308.554| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.13 r_work: 0.2978 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 28527 Z= 0.115 Angle : 0.879 84.021 38494 Z= 0.306 Chirality : 0.049 1.445 4383 Planarity : 0.004 0.048 4927 Dihedral : 4.283 56.474 3884 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.81 % Allowed : 14.59 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.26 (0.14), residues: 3497 helix: 1.26 (0.16), residues: 1218 sheet: 0.21 (0.21), residues: 571 loop : -0.59 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 79 TYR 0.014 0.001 TYR N 43 PHE 0.013 0.001 PHE B 359 TRP 0.012 0.001 TRP B 8 HIS 0.012 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00262 (28495) covalent geometry : angle 0.68123 (38458) hydrogen bonds : bond 0.03604 ( 1170) hydrogen bonds : angle 4.37420 ( 3270) metal coordination : bond 0.01527 ( 32) metal coordination : angle 18.15125 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 437 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8453 (ptpp) cc_final: 0.8234 (pttm) REVERT: A 267 ASP cc_start: 0.7280 (m-30) cc_final: 0.6697 (t0) REVERT: A 737 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7029 (tt0) REVERT: B 61 ARG cc_start: 0.8337 (ptt90) cc_final: 0.8079 (ptt90) REVERT: B 68 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6931 (ttm170) REVERT: B 171 LEU cc_start: 0.8210 (mt) cc_final: 0.7954 (mt) REVERT: B 245 GLN cc_start: 0.8192 (tt0) cc_final: 0.7971 (tt0) REVERT: B 255 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7025 (tt0) REVERT: B 458 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: B 540 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7311 (mm-30) REVERT: B 544 GLN cc_start: 0.8404 (mt0) cc_final: 0.7884 (mt0) REVERT: B 590 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6400 (mm-30) REVERT: B 594 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7351 (mttp) REVERT: B 599 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7277 (mp0) REVERT: B 759 GLU cc_start: 0.8197 (tt0) cc_final: 0.7949 (tt0) REVERT: B 835 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7421 (pt) REVERT: C 181 GLU cc_start: 0.7052 (pt0) cc_final: 0.6550 (pt0) REVERT: C 203 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.7115 (t) REVERT: C 363 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7505 (mm-30) REVERT: D 71 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: E 145 MET cc_start: 0.2288 (tpt) cc_final: 0.2071 (tmt) REVERT: E 163 MET cc_start: -0.0306 (mmp) cc_final: -0.0756 (tpp) REVERT: G 5 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8196 (tpp) REVERT: G 15 GLU cc_start: 0.7701 (mp0) cc_final: 0.7304 (mp0) REVERT: G 42 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: G 50 GLU cc_start: 0.8563 (pt0) cc_final: 0.8062 (pt0) REVERT: G 77 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: G 99 LEU cc_start: 0.7737 (mm) cc_final: 0.7464 (mm) REVERT: K 11 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8495 (mtpt) REVERT: L 21 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7416 (pp20) REVERT: N 19 GLU cc_start: 0.7211 (mp0) cc_final: 0.6696 (mp0) REVERT: Q 45 MET cc_start: 0.7066 (ttp) cc_final: 0.6549 (ttp) REVERT: Q 49 ASP cc_start: 0.7228 (m-30) cc_final: 0.6796 (m-30) REVERT: Y 14 LYS cc_start: 0.6439 (ttmt) cc_final: 0.6026 (tttm) REVERT: Y 77 LYS cc_start: 0.6907 (ptmt) cc_final: 0.6531 (ttpt) outliers start: 56 outliers final: 35 residues processed: 465 average time/residue: 0.8153 time to fit residues: 430.5747 Evaluate side-chains 475 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 429 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 61 LYS Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 199 optimal weight: 1.9990 chunk 139 optimal weight: 0.1980 chunk 137 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 0.0040 chunk 140 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN C 271 GLN C 375 GLN D 75 HIS D 94 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.168717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108150 restraints weight = 26211.386| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.11 r_work: 0.2979 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 28527 Z= 0.129 Angle : 0.893 83.927 38494 Z= 0.313 Chirality : 0.050 1.452 4383 Planarity : 0.004 0.048 4927 Dihedral : 4.313 58.166 3884 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.55 % Allowed : 14.97 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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 (0.14), residues: 3497 helix: 1.23 (0.15), residues: 1219 sheet: 0.19 (0.21), residues: 571 loop : -0.60 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 79 TYR 0.014 0.001 TYR A 850 PHE 0.014 0.001 PHE B 359 TRP 0.011 0.001 TRP B 8 HIS 0.013 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00302 (28495) covalent geometry : angle 0.69404 (38458) hydrogen bonds : bond 0.03815 ( 1170) hydrogen bonds : angle 4.38850 ( 3270) metal coordination : bond 0.01626 ( 32) metal coordination : angle 18.37317 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 431 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8249 (pttm) REVERT: A 267 ASP cc_start: 0.7294 (m-30) cc_final: 0.6714 (t0) REVERT: A 359 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: A 737 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7151 (tt0) REVERT: B 61 ARG cc_start: 0.8358 (ptt90) cc_final: 0.8051 (ptt90) REVERT: B 68 ARG cc_start: 0.7219 (ttm-80) cc_final: 0.7013 (ttm170) REVERT: B 171 LEU cc_start: 0.8262 (mt) cc_final: 0.8019 (mt) REVERT: B 245 GLN cc_start: 0.8243 (tt0) cc_final: 0.8023 (tt0) REVERT: B 255 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7121 (tt0) REVERT: B 458 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: B 540 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 544 GLN cc_start: 0.8465 (mt0) cc_final: 0.7947 (mt0) REVERT: B 590 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6477 (mm-30) REVERT: B 594 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7450 (mttp) REVERT: B 599 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7319 (mp0) REVERT: B 835 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7481 (pt) REVERT: B 891 ASP cc_start: 0.8094 (m-30) cc_final: 0.7853 (m-30) REVERT: C 35 ASP cc_start: 0.7930 (m-30) cc_final: 0.7522 (m-30) REVERT: C 44 GLU cc_start: 0.7451 (tt0) cc_final: 0.6825 (mp0) REVERT: C 181 GLU cc_start: 0.7054 (pt0) cc_final: 0.6555 (pt0) REVERT: C 203 SER cc_start: 0.7658 (OUTLIER) cc_final: 0.7172 (t) REVERT: C 363 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7594 (mm-30) REVERT: D 71 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: E 163 MET cc_start: -0.0423 (mmp) cc_final: -0.0907 (tpp) REVERT: F 76 ILE cc_start: 0.1473 (mm) cc_final: 0.0959 (tp) REVERT: G 15 GLU cc_start: 0.7722 (mp0) cc_final: 0.7350 (mp0) REVERT: G 42 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: G 50 GLU cc_start: 0.8568 (pt0) cc_final: 0.8104 (pt0) REVERT: G 77 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: G 99 LEU cc_start: 0.7808 (mm) cc_final: 0.7556 (mm) REVERT: K 11 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8550 (mtpt) REVERT: L 21 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: N 19 GLU cc_start: 0.7259 (mp0) cc_final: 0.6748 (mp0) REVERT: Q 45 MET cc_start: 0.7132 (ttp) cc_final: 0.6793 (ttm) REVERT: Q 49 ASP cc_start: 0.7291 (m-30) cc_final: 0.6856 (m-30) REVERT: Y 12 LYS cc_start: 0.6969 (ptpp) cc_final: 0.6682 (ptpp) REVERT: Y 14 LYS cc_start: 0.6497 (ttmt) cc_final: 0.6084 (tttm) REVERT: Y 77 LYS cc_start: 0.6952 (ptmt) cc_final: 0.6579 (ttpt) outliers start: 48 outliers final: 37 residues processed: 453 average time/residue: 0.8106 time to fit residues: 416.5792 Evaluate side-chains 481 residues out of total 3115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 433 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 11 LYS Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 61 LYS Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 13 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 297 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN C 271 GLN D 75 HIS D 94 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106985 restraints weight = 26283.359| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.18 r_work: 0.2968 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 28527 Z= 0.123 Angle : 0.890 83.975 38494 Z= 0.312 Chirality : 0.050 1.447 4383 Planarity : 0.004 0.048 4927 Dihedral : 4.293 58.063 3884 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.81 % Allowed : 14.81 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.26 (0.14), residues: 3497 helix: 1.26 (0.15), residues: 1218 sheet: 0.20 (0.21), residues: 571 loop : -0.59 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 79 TYR 0.014 0.001 TYR C 128 PHE 0.014 0.001 PHE B 359 TRP 0.012 0.001 TRP B 8 HIS 0.012 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00286 (28495) covalent geometry : angle 0.69159 (38458) hydrogen bonds : bond 0.03755 ( 1170) hydrogen bonds : angle 4.37389 ( 3270) metal coordination : bond 0.01539 ( 32) metal coordination : angle 18.32444 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14553.84 seconds wall clock time: 247 minutes 0.26 seconds (14820.26 seconds total)