Starting phenix.real_space_refine on Sat Mar 7 00:23:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7une_26622/03_2026/7une_26622.cif Found real_map, /net/cci-nas-00/data/ceres_data/7une_26622/03_2026/7une_26622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7une_26622/03_2026/7une_26622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7une_26622/03_2026/7une_26622.map" model { file = "/net/cci-nas-00/data/ceres_data/7une_26622/03_2026/7une_26622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7une_26622/03_2026/7une_26622.cif" } resolution = 3.73 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= 0.004 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: 4 Type Number sf(0) Gaussians S 199 5.16 5 C 22859 2.51 5 N 6303 2.21 5 O 6848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 254 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: 36209 Number of models: 1 Model: "" Number of chains: 14 Chain: "L" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "U" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3365 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 1 Chain: "d" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1818 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain: "M" Number of atoms: 4619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4619 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 564} Chain breaks: 1 Chain: "N" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4613 Classifications: {'peptide': 593} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 562} Chain breaks: 1 Chain: "Q" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3604 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "O" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "P" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3560 Classifications: {'peptide': 455} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 427} Chain breaks: 1 Chain: "b" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1479 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "c" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1505 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 189} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "g" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 665 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'GLU:plan': 8, 'ARG:plan': 8, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 142 Chain: "e" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 501 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 82 Chain: "f" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 512 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 7.90, per 1000 atoms: 0.22 Number of scatterers: 36209 At special positions: 0 Unit cell: (212.48, 157.7, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 199 16.00 O 6848 8.00 N 6303 7.00 C 22859 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: 3.17 Conformation dependent library (CDL) restraints added in 1.8 seconds 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8676 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 41 sheets defined 42.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'L' and resid 105 through 113 removed outlier: 3.977A pdb=" N SER L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER L 111 " --> pdb=" O SER L 107 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN L 112 " --> pdb=" O ASP L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 257 No H-bonds generated for 'chain 'L' and resid 255 through 257' Processing helix chain 'L' and resid 258 through 266 removed outlier: 4.051A pdb=" N SER L 264 " --> pdb=" O SER L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 291 removed outlier: 4.094A pdb=" N GLU L 286 " --> pdb=" O ASN L 282 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL L 287 " --> pdb=" O GLU L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 325 Processing helix chain 'L' and resid 326 through 339 removed outlier: 3.541A pdb=" N PHE L 337 " --> pdb=" O LEU L 333 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP L 339 " --> pdb=" O GLU L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 365 removed outlier: 3.776A pdb=" N TRP L 354 " --> pdb=" O SER L 350 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU L 360 " --> pdb=" O GLU L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 382 removed outlier: 3.556A pdb=" N ARG L 381 " --> pdb=" O TYR L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 387 removed outlier: 3.534A pdb=" N GLU L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 419 through 426 removed outlier: 3.598A pdb=" N ALA L 424 " --> pdb=" O PRO L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 458 through 460 No H-bonds generated for 'chain 'L' and resid 458 through 460' Processing helix chain 'L' and resid 461 through 469 removed outlier: 3.504A pdb=" N LYS L 467 " --> pdb=" O GLU L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 486 removed outlier: 3.889A pdb=" N THR L 477 " --> pdb=" O VAL L 473 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU L 481 " --> pdb=" O THR L 477 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU L 483 " --> pdb=" O ALA L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 490 Processing helix chain 'L' and resid 502 through 507 removed outlier: 3.616A pdb=" N ILE L 507 " --> pdb=" O GLU L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 519 removed outlier: 4.056A pdb=" N LYS L 513 " --> pdb=" O LEU L 509 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP L 517 " --> pdb=" O LYS L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 545 removed outlier: 3.986A pdb=" N ASN L 543 " --> pdb=" O GLY L 539 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET L 544 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 545 through 557 removed outlier: 3.537A pdb=" N ASP L 549 " --> pdb=" O ILE L 545 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL L 555 " --> pdb=" O ALA L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 567 through 572 Processing helix chain 'L' and resid 574 through 582 removed outlier: 3.768A pdb=" N TYR L 579 " --> pdb=" O GLY L 575 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER L 582 " --> pdb=" O LEU L 578 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 587 removed outlier: 3.825A pdb=" N LYS L 587 " --> pdb=" O MET L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 593 through 613 removed outlier: 3.793A pdb=" N LEU L 605 " --> pdb=" O TYR L 601 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG L 613 " --> pdb=" O GLN L 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 65 removed outlier: 3.612A pdb=" N THR D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 23 " --> pdb=" O MET D 19 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY D 29 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 77 removed outlier: 4.839A pdb=" N THR D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 removed outlier: 3.578A pdb=" N VAL D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 174 removed outlier: 3.535A pdb=" N ALA D 132 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 removed outlier: 3.627A pdb=" N ARG D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 29 removed outlier: 4.160A pdb=" N GLU U 23 " --> pdb=" O GLU U 19 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP U 25 " --> pdb=" O GLN U 21 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU U 27 " --> pdb=" O GLU U 23 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 51 removed outlier: 3.882A pdb=" N LEU U 50 " --> pdb=" O SER U 46 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN U 51 " --> pdb=" O LEU U 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 46 through 51' Processing helix chain 'U' and resid 59 through 71 removed outlier: 3.554A pdb=" N VAL U 63 " --> pdb=" O PRO U 59 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR U 64 " --> pdb=" O PRO U 60 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG U 65 " --> pdb=" O GLU U 61 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET U 70 " --> pdb=" O LEU U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 99 removed outlier: 3.690A pdb=" N ALA U 93 " --> pdb=" O GLU U 89 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER U 94 " --> pdb=" O GLN U 90 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 107 removed outlier: 3.609A pdb=" N SER U 107 " --> pdb=" O SER U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 112 Processing helix chain 'U' and resid 124 through 144 removed outlier: 3.537A pdb=" N LYS U 128 " --> pdb=" O ARG U 124 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL U 134 " --> pdb=" O THR U 130 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER U 136 " --> pdb=" O ASP U 132 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL U 138 " --> pdb=" O VAL U 134 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS U 139 " --> pdb=" O GLY U 135 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER U 142 " --> pdb=" O VAL U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 170 removed outlier: 3.656A pdb=" N GLN U 163 " --> pdb=" O ASN U 159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN U 168 " --> pdb=" O VAL U 164 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU U 169 " --> pdb=" O LEU U 165 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU U 170 " --> pdb=" O ALA U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 187 removed outlier: 4.235A pdb=" N LEU U 187 " --> pdb=" O PRO U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 192 through 197 removed outlier: 3.691A pdb=" N GLU U 197 " --> pdb=" O ARG U 193 " (cutoff:3.500A) Processing helix chain 'U' and resid 198 through 203 Processing helix chain 'U' and resid 203 through 209 removed outlier: 3.987A pdb=" N ALA U 207 " --> pdb=" O VAL U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 218 removed outlier: 3.561A pdb=" N ILE U 214 " --> pdb=" O LEU U 210 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS U 215 " --> pdb=" O SER U 211 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS U 216 " --> pdb=" O VAL U 212 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY U 217 " --> pdb=" O VAL U 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 247 through 255 removed outlier: 3.665A pdb=" N ASN U 255 " --> pdb=" O VAL U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 259 through 263 removed outlier: 3.532A pdb=" N GLN U 262 " --> pdb=" O PRO U 259 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG U 263 " --> pdb=" O ARG U 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 259 through 263' Processing helix chain 'U' and resid 278 through 286 Processing helix chain 'U' and resid 432 through 440 Processing helix chain 'd' and resid 4 through 12 removed outlier: 3.527A pdb=" N VAL d 8 " --> pdb=" O SER d 4 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS d 10 " --> pdb=" O ALA d 6 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN d 11 " --> pdb=" O ASP d 7 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 32 through 47 removed outlier: 3.805A pdb=" N GLU d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU d 37 " --> pdb=" O LYS d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 72 removed outlier: 3.555A pdb=" N LYS d 62 " --> pdb=" O GLU d 58 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU d 65 " --> pdb=" O GLU d 61 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE d 70 " --> pdb=" O GLN d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 87 removed outlier: 4.137A pdb=" N LYS d 82 " --> pdb=" O GLN d 78 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG d 85 " --> pdb=" O LEU d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 108 removed outlier: 3.603A pdb=" N LYS d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG d 101 " --> pdb=" O GLU d 97 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS d 104 " --> pdb=" O GLN d 100 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL d 105 " --> pdb=" O ARG d 101 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL d 106 " --> pdb=" O LEU d 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP d 108 " --> pdb=" O LYS d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 128 removed outlier: 3.928A pdb=" N VAL d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY d 118 " --> pdb=" O VAL d 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN d 126 " --> pdb=" O GLN d 122 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU d 128 " --> pdb=" O LEU d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 149 removed outlier: 3.533A pdb=" N ALA d 146 " --> pdb=" O PRO d 142 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA d 147 " --> pdb=" O LEU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 150 through 156 removed outlier: 4.033A pdb=" N VAL d 154 " --> pdb=" O LYS d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 216 removed outlier: 3.802A pdb=" N ASP d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU d 202 " --> pdb=" O SER d 198 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN d 205 " --> pdb=" O ASP d 201 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN d 206 " --> pdb=" O LEU d 202 " (cutoff:3.500A) Proline residue: d 209 - end of helix Processing helix chain 'M' and resid 105 through 113 removed outlier: 4.195A pdb=" N SER M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR M 113 " --> pdb=" O ILE M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 265 removed outlier: 3.776A pdb=" N GLN M 261 " --> pdb=" O THR M 257 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER M 262 " --> pdb=" O VAL M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 291 removed outlier: 3.550A pdb=" N VAL M 287 " --> pdb=" O GLU M 283 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 288 " --> pdb=" O MET M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 339 removed outlier: 3.650A pdb=" N GLU M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER M 326 " --> pdb=" O ALA M 322 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE M 327 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR M 328 " --> pdb=" O GLU M 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP M 339 " --> pdb=" O GLU M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 364 Processing helix chain 'M' and resid 377 through 382 Processing helix chain 'M' and resid 382 through 387 Processing helix chain 'M' and resid 412 through 416 removed outlier: 3.948A pdb=" N GLY M 415 " --> pdb=" O PRO M 412 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP M 416 " --> pdb=" O PRO M 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 412 through 416' Processing helix chain 'M' and resid 421 through 426 Processing helix chain 'M' and resid 461 through 469 removed outlier: 3.698A pdb=" N LYS M 467 " --> pdb=" O GLU M 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 471 through 494 removed outlier: 3.770A pdb=" N LEU M 475 " --> pdb=" O GLU M 471 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS M 478 " --> pdb=" O PRO M 474 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 483 " --> pdb=" O ALA M 479 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP M 488 " --> pdb=" O GLN M 484 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU M 491 " --> pdb=" O GLU M 487 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE M 492 " --> pdb=" O ASP M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 507 through 519 removed outlier: 3.573A pdb=" N ALA M 512 " --> pdb=" O THR M 508 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS M 513 " --> pdb=" O LEU M 509 " (cutoff:3.500A) Processing helix chain 'M' and resid 533 through 557 removed outlier: 3.562A pdb=" N ASN M 543 " --> pdb=" O GLY M 539 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET M 544 " --> pdb=" O MET M 540 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU M 556 " --> pdb=" O ARG M 552 " (cutoff:3.500A) Processing helix chain 'M' and resid 566 through 574 removed outlier: 3.637A pdb=" N ILE M 570 " --> pdb=" O THR M 566 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS M 573 " --> pdb=" O ILE M 569 " (cutoff:3.500A) Processing helix chain 'M' and resid 576 through 582 Processing helix chain 'M' and resid 597 through 609 removed outlier: 3.611A pdb=" N ALA M 602 " --> pdb=" O LYS M 598 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN M 603 " --> pdb=" O ALA M 599 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU M 604 " --> pdb=" O ASP M 600 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 612 No H-bonds generated for 'chain 'M' and resid 610 through 612' Processing helix chain 'N' and resid 105 through 113 removed outlier: 3.565A pdb=" N SER N 110 " --> pdb=" O LEU N 106 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 266 removed outlier: 3.734A pdb=" N LEU N 263 " --> pdb=" O ILE N 259 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS N 265 " --> pdb=" O GLN N 261 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR N 266 " --> pdb=" O SER N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 280 through 291 removed outlier: 4.227A pdb=" N VAL N 287 " --> pdb=" O GLU N 283 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG N 289 " --> pdb=" O SER N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 340 removed outlier: 3.553A pdb=" N GLU N 324 " --> pdb=" O VAL N 320 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA N 325 " --> pdb=" O ALA N 321 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER N 326 " --> pdb=" O ALA N 322 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE N 327 " --> pdb=" O ARG N 323 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR N 328 " --> pdb=" O GLU N 324 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE N 337 " --> pdb=" O LEU N 333 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET N 340 " --> pdb=" O TYR N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 365 removed outlier: 3.849A pdb=" N GLU N 360 " --> pdb=" O GLU N 356 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 387 removed outlier: 3.518A pdb=" N GLU N 387 " --> pdb=" O ALA N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 437 through 441 removed outlier: 4.106A pdb=" N GLN N 441 " --> pdb=" O LYS N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 462 removed outlier: 3.563A pdb=" N ASP N 462 " --> pdb=" O ARG N 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 459 through 462' Processing helix chain 'N' and resid 463 through 469 Processing helix chain 'N' and resid 471 through 486 removed outlier: 3.982A pdb=" N LEU N 475 " --> pdb=" O GLU N 471 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU N 481 " --> pdb=" O THR N 477 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU N 483 " --> pdb=" O ALA N 479 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN N 484 " --> pdb=" O LYS N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 486 through 496 removed outlier: 3.831A pdb=" N GLU N 491 " --> pdb=" O GLU N 487 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE N 492 " --> pdb=" O ASP N 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 506 through 519 removed outlier: 4.607A pdb=" N ALA N 512 " --> pdb=" O THR N 508 " (cutoff:3.500A) Processing helix chain 'N' and resid 533 through 558 removed outlier: 3.624A pdb=" N LEU N 541 " --> pdb=" O THR N 537 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN N 543 " --> pdb=" O GLY N 539 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA N 546 " --> pdb=" O SER N 542 " (cutoff:3.500A) Processing helix chain 'N' and resid 566 through 568 No H-bonds generated for 'chain 'N' and resid 566 through 568' Processing helix chain 'N' and resid 569 through 574 removed outlier: 3.734A pdb=" N HIS N 573 " --> pdb=" O ILE N 569 " (cutoff:3.500A) Processing helix chain 'N' and resid 576 through 581 removed outlier: 3.710A pdb=" N LYS N 580 " --> pdb=" O GLU N 576 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 604 Processing helix chain 'N' and resid 605 through 610 Processing helix chain 'N' and resid 611 through 615 Processing helix chain 'Q' and resid 124 through 128 removed outlier: 3.919A pdb=" N MET Q 127 " --> pdb=" O SER Q 124 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU Q 128 " --> pdb=" O GLU Q 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 124 through 128' Processing helix chain 'Q' and resid 159 through 161 No H-bonds generated for 'chain 'Q' and resid 159 through 161' Processing helix chain 'Q' and resid 174 through 179 Processing helix chain 'Q' and resid 200 through 210 Processing helix chain 'Q' and resid 237 through 246 Processing helix chain 'Q' and resid 269 through 286 Proline residue: Q 275 - end of helix removed outlier: 3.709A pdb=" N LEU Q 279 " --> pdb=" O PRO Q 275 " (cutoff:3.500A) Processing helix chain 'Q' and resid 300 through 314 removed outlier: 3.540A pdb=" N ARG Q 314 " --> pdb=" O VAL Q 310 " (cutoff:3.500A) Processing helix chain 'Q' and resid 319 through 323 removed outlier: 4.003A pdb=" N GLY Q 322 " --> pdb=" O GLY Q 319 " (cutoff:3.500A) Processing helix chain 'Q' and resid 324 through 325 No H-bonds generated for 'chain 'Q' and resid 324 through 325' Processing helix chain 'Q' and resid 326 through 336 removed outlier: 3.930A pdb=" N ILE Q 334 " --> pdb=" O ASP Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 360 Processing helix chain 'Q' and resid 363 through 370 Processing helix chain 'Q' and resid 414 through 440 removed outlier: 4.003A pdb=" N ASN Q 420 " --> pdb=" O ALA Q 416 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA Q 424 " --> pdb=" O ASN Q 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY Q 429 " --> pdb=" O CYS Q 425 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA Q 437 " --> pdb=" O GLN Q 433 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL Q 438 " --> pdb=" O ALA Q 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 449 through 462 removed outlier: 3.683A pdb=" N LEU Q 455 " --> pdb=" O TYR Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 473 through 485 removed outlier: 3.560A pdb=" N ASP Q 478 " --> pdb=" O TYR Q 474 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE Q 479 " --> pdb=" O GLU Q 475 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN Q 482 " --> pdb=" O ASP Q 478 " (cutoff:3.500A) Processing helix chain 'Q' and resid 496 through 504 removed outlier: 4.596A pdb=" N GLU Q 502 " --> pdb=" O SER Q 498 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 128 removed outlier: 3.735A pdb=" N MET O 127 " --> pdb=" O SER O 124 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU O 128 " --> pdb=" O GLU O 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 124 through 128' Processing helix chain 'O' and resid 159 through 161 No H-bonds generated for 'chain 'O' and resid 159 through 161' Processing helix chain 'O' and resid 174 through 179 Processing helix chain 'O' and resid 198 through 210 removed outlier: 3.523A pdb=" N GLN O 209 " --> pdb=" O GLN O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 251 removed outlier: 3.622A pdb=" N PHE O 243 " --> pdb=" O GLU O 239 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER O 246 " --> pdb=" O ARG O 242 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU O 249 " --> pdb=" O LYS O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 288 removed outlier: 3.582A pdb=" N TYR O 287 " --> pdb=" O GLU O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 313 removed outlier: 3.527A pdb=" N ALA O 304 " --> pdb=" O MET O 300 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU O 309 " --> pdb=" O GLU O 305 " (cutoff:3.500A) Processing helix chain 'O' and resid 319 through 323 Processing helix chain 'O' and resid 324 through 326 No H-bonds generated for 'chain 'O' and resid 324 through 326' Processing helix chain 'O' and resid 327 through 336 removed outlier: 4.020A pdb=" N THR O 333 " --> pdb=" O THR O 329 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 360 Processing helix chain 'O' and resid 363 through 373 removed outlier: 3.554A pdb=" N LEU O 368 " --> pdb=" O PRO O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 380 through 385 removed outlier: 3.597A pdb=" N HIS O 384 " --> pdb=" O ASP O 380 " (cutoff:3.500A) Processing helix chain 'O' and resid 401 through 406 removed outlier: 3.573A pdb=" N ILE O 406 " --> pdb=" O MET O 402 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 440 removed outlier: 3.617A pdb=" N SER O 419 " --> pdb=" O HIS O 415 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN O 420 " --> pdb=" O ALA O 416 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN O 421 " --> pdb=" O ASP O 417 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA O 434 " --> pdb=" O LYS O 430 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA O 437 " --> pdb=" O GLN O 433 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL O 438 " --> pdb=" O ALA O 434 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 459 removed outlier: 3.780A pdb=" N LYS O 457 " --> pdb=" O GLU O 453 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU O 459 " --> pdb=" O LEU O 455 " (cutoff:3.500A) Processing helix chain 'O' and resid 474 through 482 removed outlier: 3.926A pdb=" N ASP O 478 " --> pdb=" O TYR O 474 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY O 480 " --> pdb=" O THR O 476 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 504 removed outlier: 3.812A pdb=" N GLU O 502 " --> pdb=" O SER O 498 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 161 No H-bonds generated for 'chain 'P' and resid 159 through 161' Processing helix chain 'P' and resid 198 through 210 Processing helix chain 'P' and resid 237 through 251 Processing helix chain 'P' and resid 253 through 255 No H-bonds generated for 'chain 'P' and resid 253 through 255' Processing helix chain 'P' and resid 267 through 272 removed outlier: 3.678A pdb=" N GLU P 270 " --> pdb=" O PRO P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 288 removed outlier: 3.614A pdb=" N THR P 281 " --> pdb=" O LEU P 277 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR P 287 " --> pdb=" O GLU P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 313 removed outlier: 3.623A pdb=" N ALA P 304 " --> pdb=" O MET P 300 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA P 306 " --> pdb=" O SER P 302 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL P 310 " --> pdb=" O ALA P 306 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA P 313 " --> pdb=" O GLU P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 319 through 323 removed outlier: 3.656A pdb=" N GLY P 322 " --> pdb=" O GLY P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 325 No H-bonds generated for 'chain 'P' and resid 324 through 325' Processing helix chain 'P' and resid 326 through 336 removed outlier: 3.647A pdb=" N GLU P 336 " --> pdb=" O ALA P 332 " (cutoff:3.500A) Processing helix chain 'P' and resid 356 through 360 Processing helix chain 'P' and resid 363 through 370 Processing helix chain 'P' and resid 381 through 386 removed outlier: 3.608A pdb=" N ARG P 386 " --> pdb=" O GLN P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 440 removed outlier: 3.649A pdb=" N ASN P 420 " --> pdb=" O ALA P 416 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 424 " --> pdb=" O ASN P 420 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP P 431 " --> pdb=" O ALA P 427 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA P 434 " --> pdb=" O LYS P 430 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL P 438 " --> pdb=" O ALA P 434 " (cutoff:3.500A) Processing helix chain 'P' and resid 450 through 462 removed outlier: 3.627A pdb=" N LEU P 455 " --> pdb=" O TYR P 451 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN P 456 " --> pdb=" O LEU P 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 459 " --> pdb=" O LEU P 455 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG P 460 " --> pdb=" O GLN P 456 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN P 461 " --> pdb=" O LYS P 457 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 483 removed outlier: 3.577A pdb=" N LEU P 477 " --> pdb=" O VAL P 473 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN P 482 " --> pdb=" O ASP P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 488 through 492 removed outlier: 3.536A pdb=" N MET P 491 " --> pdb=" O PRO P 488 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU P 492 " --> pdb=" O LYS P 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 488 through 492' Processing helix chain 'P' and resid 496 through 504 removed outlier: 4.485A pdb=" N GLU P 502 " --> pdb=" O SER P 498 " (cutoff:3.500A) Processing helix chain 'b' and resid 47 through 59 removed outlier: 3.675A pdb=" N LEU b 51 " --> pdb=" O GLN b 47 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE b 53 " --> pdb=" O GLN b 49 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR b 56 " --> pdb=" O LYS b 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS b 59 " --> pdb=" O GLU b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 60 through 101 removed outlier: 3.795A pdb=" N GLU b 65 " --> pdb=" O GLU b 61 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN b 66 " --> pdb=" O LYS b 62 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN b 71 " --> pdb=" O GLN b 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN b 78 " --> pdb=" O ASN b 74 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU b 90 " --> pdb=" O ALA b 86 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE b 91 " --> pdb=" O ARG b 87 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN b 96 " --> pdb=" O THR b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 112 through 128 removed outlier: 4.069A pdb=" N GLY b 118 " --> pdb=" O VAL b 114 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU b 121 " --> pdb=" O ASP b 117 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU b 128 " --> pdb=" O LEU b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 150 removed outlier: 3.580A pdb=" N ALA b 147 " --> pdb=" O LEU b 143 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 160 removed outlier: 3.715A pdb=" N ALA b 158 " --> pdb=" O VAL b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 206 removed outlier: 3.756A pdb=" N LEU b 202 " --> pdb=" O SER b 198 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN b 205 " --> pdb=" O ASP b 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN b 206 " --> pdb=" O LEU b 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 216 Processing helix chain 'c' and resid 33 through 102 removed outlier: 4.269A pdb=" N GLU c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE c 38 " --> pdb=" O ALA c 34 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN c 39 " --> pdb=" O GLU c 35 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU c 41 " --> pdb=" O GLU c 37 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY c 43 " --> pdb=" O ASN c 39 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU c 45 " --> pdb=" O GLU c 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL c 46 " --> pdb=" O LYS c 42 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN c 49 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU c 51 " --> pdb=" O GLN c 47 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS c 52 " --> pdb=" O THR c 48 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU c 55 " --> pdb=" O LEU c 51 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR c 57 " --> pdb=" O ILE c 53 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU c 58 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS c 62 " --> pdb=" O GLU c 58 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG c 80 " --> pdb=" O MET c 76 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN c 100 " --> pdb=" O ASN c 96 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 removed outlier: 4.146A pdb=" N GLY c 118 " --> pdb=" O VAL c 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU c 121 " --> pdb=" O ASP c 117 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY c 123 " --> pdb=" O LEU c 119 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 149 removed outlier: 3.639A pdb=" N ALA c 146 " --> pdb=" O PRO c 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN c 149 " --> pdb=" O LYS c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 151 through 158 removed outlier: 3.788A pdb=" N VAL c 157 " --> pdb=" O PRO c 153 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 204 Processing helix chain 'c' and resid 207 through 216 Processing helix chain 'g' and resid 10 through 20 removed outlier: 3.891A pdb=" N ARG g 17 " --> pdb=" O GLN g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 28 through 33 removed outlier: 3.657A pdb=" N LEU g 33 " --> pdb=" O LYS g 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 45 Processing helix chain 'g' and resid 47 through 66 removed outlier: 3.753A pdb=" N GLN g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 72 removed outlier: 3.774A pdb=" N ALA g 71 " --> pdb=" O ASN g 68 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU g 72 " --> pdb=" O LEU g 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 68 through 72' Processing helix chain 'g' and resid 77 through 90 removed outlier: 3.778A pdb=" N SER g 86 " --> pdb=" O GLN g 82 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER g 87 " --> pdb=" O GLY g 83 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN g 89 " --> pdb=" O GLN g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 104 removed outlier: 3.869A pdb=" N ALA g 97 " --> pdb=" O GLU g 93 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS g 104 " --> pdb=" O LEU g 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 43 Processing helix chain 'e' and resid 46 through 50 Processing helix chain 'e' and resid 51 through 56 Processing helix chain 'e' and resid 56 through 87 removed outlier: 3.555A pdb=" N GLN e 60 " --> pdb=" O GLN e 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA e 61 " --> pdb=" O SER e 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET e 63 " --> pdb=" O GLN e 59 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER e 65 " --> pdb=" O ALA e 61 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN e 66 " --> pdb=" O ALA e 62 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY e 67 " --> pdb=" O MET e 63 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN e 68 " --> pdb=" O GLY e 64 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER e 70 " --> pdb=" O GLN e 66 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA e 71 " --> pdb=" O GLY e 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU e 72 " --> pdb=" O ASN e 68 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL e 73 " --> pdb=" O LEU e 69 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL e 81 " --> pdb=" O THR e 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET e 84 " --> pdb=" O GLN e 80 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER e 87 " --> pdb=" O GLY e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 91 through 104 removed outlier: 3.598A pdb=" N ALA e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 55 Processing helix chain 'f' and resid 59 through 68 removed outlier: 3.692A pdb=" N SER f 65 " --> pdb=" O ALA f 61 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN f 66 " --> pdb=" O ALA f 62 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 85 removed outlier: 3.877A pdb=" N GLU f 72 " --> pdb=" O ASN f 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR f 77 " --> pdb=" O VAL f 73 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG f 78 " --> pdb=" O GLU f 74 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG f 79 " --> pdb=" O GLN f 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN f 80 " --> pdb=" O ALA f 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 18 through 25 removed outlier: 6.849A pdb=" N THR L 30 " --> pdb=" O HIS L 22 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL L 24 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL L 28 " --> pdb=" O VAL L 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 28 through 32 current: chain 'L' and resid 50 through 58 removed outlier: 5.953A pdb=" N ILE L 54 " --> pdb=" O GLN L 65 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN L 65 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG L 56 " --> pdb=" O THR L 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 61 through 66 current: chain 'd' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 164 through 167 current: chain 'd' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 190 through 195 current: chain 'M' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 28 through 32 current: chain 'M' and resid 50 through 58 removed outlier: 6.497A pdb=" N THR M 63 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU M 57 " --> pdb=" O MET M 61 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 61 through 66 current: chain 'Q' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 57 through 60 current: chain 'Q' and resid 84 through 90 removed outlier: 6.760A pdb=" N VAL Q 95 " --> pdb=" O LEU Q 87 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL Q 89 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS Q 93 " --> pdb=" O VAL Q 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 93 through 98 current: chain 'P' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 60 current: chain 'P' and resid 81 through 90 removed outlier: 6.622A pdb=" N VAL P 95 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL P 89 " --> pdb=" O LYS P 93 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS P 93 " --> pdb=" O VAL P 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'L' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 98 through 99 current: chain 'L' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 309 through 315 current: chain 'L' and resid 401 through 407 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 164 through 167 removed outlier: 6.452A pdb=" N HIS L 164 " --> pdb=" O ILE L 155 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE L 155 " --> pdb=" O HIS L 164 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE L 166 " --> pdb=" O TYR L 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 146 through 147 removed outlier: 6.674A pdb=" N GLU L 193 " --> pdb=" O THR L 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 295 through 297 Processing sheet with id=AA7, first strand: chain 'L' and resid 431 through 432 Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 98 Processing sheet with id=AA9, first strand: chain 'U' and resid 44 through 45 removed outlier: 3.560A pdb=" N VAL U 86 " --> pdb=" O PHE U 45 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 121 through 122 Processing sheet with id=AB2, first strand: chain 'U' and resid 233 through 235 removed outlier: 6.053A pdb=" N GLU U 233 " --> pdb=" O TRP U 266 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU U 268 " --> pdb=" O GLU U 233 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLN U 235 " --> pdb=" O LEU U 268 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE U 270 " --> pdb=" O GLN U 235 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU U 268 " --> pdb=" O ALA U 410 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA U 410 " --> pdb=" O LEU U 268 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS U 405 " --> pdb=" O GLU U 297 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY U 305 " --> pdb=" O PHE U 327 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA U 334 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 315 through 319 removed outlier: 6.266A pdb=" N GLN U 317 " --> pdb=" O LEU U 348 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU U 348 " --> pdb=" O GLN U 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 87 through 90 Processing sheet with id=AB5, first strand: chain 'M' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 98 through 99 current: chain 'M' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 309 through 315 current: chain 'M' and resid 403 through 407 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'M' and resid 133 through 134 Processing sheet with id=AB7, first strand: chain 'M' and resid 146 through 147 Processing sheet with id=AB8, first strand: chain 'M' and resid 152 through 157 removed outlier: 3.516A pdb=" N GLY M 154 " --> pdb=" O ILE M 166 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 226 through 227 removed outlier: 4.645A pdb=" N CYS M 240 " --> pdb=" O LEU M 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 295 through 297 Processing sheet with id=AC2, first strand: chain 'M' and resid 431 through 432 Processing sheet with id=AC3, first strand: chain 'b' and resid 166 through 167 removed outlier: 3.583A pdb=" N LYS b 191 " --> pdb=" O THR O 46 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU O 45 " --> pdb=" O PHE O 114 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE O 71 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU O 70 " --> pdb=" O VAL O 86 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL O 95 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL O 89 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS O 93 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA O 94 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU O 57 " --> pdb=" O VAL O 53 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL O 53 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE O 59 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE N 54 " --> pdb=" O GLN N 65 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN N 65 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL N 24 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR N 30 " --> pdb=" O HIS N 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU N 80 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU N 42 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU N 41 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 87 through 90 Processing sheet with id=AC5, first strand: chain 'N' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 98 through 99 current: chain 'N' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 309 through 312 current: chain 'N' and resid 401 through 408 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'N' and resid 135 through 137 removed outlier: 3.621A pdb=" N GLY N 154 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 146 through 147 removed outlier: 6.509A pdb=" N GLU N 193 " --> pdb=" O THR N 177 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 295 through 297 Processing sheet with id=AC9, first strand: chain 'N' and resid 431 through 432 Processing sheet with id=AD1, first strand: chain 'Q' and resid 120 through 123 removed outlier: 3.787A pdb=" N VAL Q 123 " --> pdb=" O ASP Q 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP Q 149 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 131 through 132 removed outlier: 8.892A pdb=" N CYS Q 258 " --> pdb=" O PHE Q 227 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE Q 229 " --> pdb=" O CYS Q 258 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE Q 260 " --> pdb=" O ILE Q 229 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE Q 231 " --> pdb=" O PHE Q 260 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN Q 262 " --> pdb=" O PHE Q 231 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA Q 233 " --> pdb=" O ASN Q 262 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL Q 293 " --> pdb=" O THR Q 349 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE Q 351 " --> pdb=" O VAL Q 293 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL Q 295 " --> pdb=" O ILE Q 351 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 163 through 164 removed outlier: 4.289A pdb=" N ARG Q 340 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 169 through 170 removed outlier: 4.422A pdb=" N ILE Q 183 " --> pdb=" O ILE Q 170 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 375 through 376 Processing sheet with id=AD6, first strand: chain 'O' and resid 120 through 123 Processing sheet with id=AD7, first strand: chain 'O' and resid 131 through 133 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 131 through 133 current: chain 'O' and resid 257 through 263 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 257 through 263 current: chain 'O' and resid 347 through 355 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'O' and resid 169 through 170 removed outlier: 4.657A pdb=" N ILE O 183 " --> pdb=" O ILE O 170 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 375 through 376 Processing sheet with id=AE1, first strand: chain 'P' and resid 120 through 123 removed outlier: 3.515A pdb=" N ASP P 149 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 131 through 133 removed outlier: 6.715A pdb=" N PHE P 132 " --> pdb=" O LEU P 261 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU P 263 " --> pdb=" O PHE P 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET P 234 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL P 293 " --> pdb=" O THR P 349 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE P 351 " --> pdb=" O VAL P 293 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL P 295 " --> pdb=" O ILE P 351 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY P 346 " --> pdb=" O VAL P 341 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL P 341 " --> pdb=" O GLY P 346 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG P 340 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE P 164 " --> pdb=" O ARG P 340 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 169 through 170 removed outlier: 4.504A pdb=" N ILE P 183 " --> pdb=" O ILE P 170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 191 through 192 Processing sheet with id=AE5, first strand: chain 'c' and resid 164 through 167 1199 hydrogen bonds defined for protein. 3435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.10 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11615 1.34 - 1.46: 6288 1.46 - 1.58: 18605 1.58 - 1.70: 0 1.70 - 1.82: 346 Bond restraints: 36854 Sorted by residual: bond pdb=" C ARG U 263 " pdb=" N HIS U 264 " ideal model delta sigma weight residual 1.333 1.390 -0.056 1.43e-02 4.89e+03 1.55e+01 bond pdb=" C TYR Q 504 " pdb=" N PRO Q 505 " ideal model delta sigma weight residual 1.333 1.376 -0.043 1.17e-02 7.31e+03 1.36e+01 bond pdb=" C HIS U 380 " pdb=" N SER U 381 " ideal model delta sigma weight residual 1.333 1.291 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C TYR O 504 " pdb=" N PRO O 505 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.97e+00 bond pdb=" CB VAL M 24 " pdb=" CG2 VAL M 24 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.27e+00 ... (remaining 36849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 49403 3.53 - 7.07: 392 7.07 - 10.60: 40 10.60 - 14.13: 3 14.13 - 17.66: 2 Bond angle restraints: 49840 Sorted by residual: angle pdb=" C ALA c 151 " pdb=" N ILE c 152 " pdb=" CA ILE c 152 " ideal model delta sigma weight residual 120.24 125.26 -5.02 6.30e-01 2.52e+00 6.36e+01 angle pdb=" C PHE N 472 " pdb=" N VAL N 473 " pdb=" CA VAL N 473 " ideal model delta sigma weight residual 120.24 124.45 -4.21 6.30e-01 2.52e+00 4.46e+01 angle pdb=" CA LEU M 234 " pdb=" CB LEU M 234 " pdb=" CG LEU M 234 " ideal model delta sigma weight residual 116.30 133.96 -17.66 3.50e+00 8.16e-02 2.55e+01 angle pdb=" C LYS c 107 " pdb=" N ASP c 108 " pdb=" CA ASP c 108 " ideal model delta sigma weight residual 121.54 131.12 -9.58 1.91e+00 2.74e-01 2.52e+01 angle pdb=" CA LEU L 234 " pdb=" CB LEU L 234 " pdb=" CG LEU L 234 " ideal model delta sigma weight residual 116.30 133.85 -17.55 3.50e+00 8.16e-02 2.52e+01 ... (remaining 49835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19896 17.97 - 35.93: 2178 35.93 - 53.90: 358 53.90 - 71.86: 80 71.86 - 89.83: 38 Dihedral angle restraints: 22550 sinusoidal: 9067 harmonic: 13483 Sorted by residual: dihedral pdb=" CA TYR b 57 " pdb=" C TYR b 57 " pdb=" N GLU b 58 " pdb=" CA GLU b 58 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA PHE N 445 " pdb=" C PHE N 445 " pdb=" N PRO N 446 " pdb=" CA PRO N 446 " ideal model delta harmonic sigma weight residual 0.00 28.44 -28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA GLU d 29 " pdb=" C GLU d 29 " pdb=" N ILE d 30 " pdb=" CA ILE d 30 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 22547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4708 0.075 - 0.150: 834 0.150 - 0.225: 66 0.225 - 0.301: 7 0.301 - 0.376: 1 Chirality restraints: 5616 Sorted by residual: chirality pdb=" CB VAL O 213 " pdb=" CA VAL O 213 " pdb=" CG1 VAL O 213 " pdb=" CG2 VAL O 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB VAL P 213 " pdb=" CA VAL P 213 " pdb=" CG1 VAL P 213 " pdb=" CG2 VAL P 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE O 59 " pdb=" CA ILE O 59 " pdb=" CG1 ILE O 59 " pdb=" CG2 ILE O 59 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 5613 not shown) Planarity restraints: 6505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL Q 317 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO Q 318 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO Q 318 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 318 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET c 208 " -0.049 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO c 209 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO c 209 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO c 209 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET d 208 " -0.049 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO d 209 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO d 209 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO d 209 " -0.041 5.00e-02 4.00e+02 ... (remaining 6502 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 8634 2.78 - 3.31: 30776 3.31 - 3.84: 58924 3.84 - 4.37: 71290 4.37 - 4.90: 121158 Nonbonded interactions: 290782 Sorted by model distance: nonbonded pdb=" OH TYR Q 287 " pdb=" O GLY Q 339 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR c 112 " pdb=" OD2 ASP c 140 " model vdw 2.262 3.040 nonbonded pdb=" O GLY P 55 " pdb=" OG1 THR P 102 " model vdw 2.284 3.040 nonbonded pdb=" O LEU O 395 " pdb=" OH TYR O 423 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR O 303 " pdb=" OD2 ASP O 330 " model vdw 2.289 3.040 ... (remaining 290777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'L' and (resid 17 through 248 or resid 257 through 616)) selection = (chain 'M' and (resid 17 through 248 or resid 257 through 616)) selection = (chain 'N' and (resid 17 through 248 or resid 257 through 616)) } ncs_group { reference = (chain 'O' and (resid 39 through 213 or resid 227 through 506)) selection = chain 'P' selection = (chain 'Q' and (resid 39 through 213 or resid 227 through 506)) } ncs_group { reference = (chain 'b' and ((resid 45 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 226)) selection = (chain 'c' and resid 45 through 226) } ncs_group { reference = (chain 'e' and ((resid 39 through 72 and (name N or name CA or name C or name O \ or name CB )) or resid 73 through 113)) selection = (chain 'f' and resid 39 through 113) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.850 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 35.620 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.007 0.074 36854 Z= 0.325 Angle : 0.965 17.664 49840 Z= 0.554 Chirality : 0.057 0.376 5616 Planarity : 0.007 0.083 6505 Dihedral : 15.557 89.827 13874 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.47 % Allowed : 9.65 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -5.40 (0.09), residues: 4623 helix: -4.62 (0.05), residues: 1899 sheet: -2.51 (0.19), residues: 622 loop : -2.74 (0.11), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG Q 321 TYR 0.021 0.002 TYR O 378 PHE 0.026 0.003 PHE L 291 TRP 0.029 0.003 TRP L 450 HIS 0.010 0.002 HIS U 445 Details of bonding type rmsd covalent geometry : bond 0.00746 (36854) covalent geometry : angle 0.96527 (49840) hydrogen bonds : bond 0.31206 ( 1199) hydrogen bonds : angle 11.12440 ( 3435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 771 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 151 ASP cc_start: 0.7542 (m-30) cc_final: 0.7193 (m-30) REVERT: L 200 LYS cc_start: 0.5867 (ttmt) cc_final: 0.5336 (pttm) REVERT: L 235 ASP cc_start: 0.7934 (m-30) cc_final: 0.7644 (m-30) REVERT: L 484 GLN cc_start: 0.5769 (tp-100) cc_final: 0.5161 (tt0) REVERT: L 540 MET cc_start: 0.8320 (mtp) cc_final: 0.7605 (mtp) REVERT: L 604 LEU cc_start: 0.5764 (tp) cc_final: 0.5493 (tp) REVERT: D 13 ARG cc_start: 0.7023 (tpt90) cc_final: 0.6477 (tpt170) REVERT: D 34 LYS cc_start: 0.7374 (tptm) cc_final: 0.6914 (mmmt) REVERT: D 56 MET cc_start: 0.4721 (mmt) cc_final: 0.4249 (ppp) REVERT: D 140 LYS cc_start: 0.4599 (pttt) cc_final: 0.4372 (ttmm) REVERT: U 70 MET cc_start: 0.3352 (ttp) cc_final: 0.2975 (tpp) REVERT: U 72 ARG cc_start: 0.3263 (mtt90) cc_final: 0.2775 (ttm110) REVERT: U 124 ARG cc_start: 0.5832 (ttt180) cc_final: 0.5413 (ttt-90) REVERT: U 243 GLU cc_start: 0.3652 (pp20) cc_final: 0.3354 (mt-10) REVERT: U 333 MET cc_start: 0.7658 (mtt) cc_final: 0.7352 (mtt) REVERT: d 20 GLU cc_start: 0.5412 (mm-30) cc_final: 0.5147 (mm-30) REVERT: d 70 ILE cc_start: 0.8353 (mm) cc_final: 0.7928 (mt) REVERT: d 111 ARG cc_start: 0.6306 (ttp-110) cc_final: 0.5678 (mtp180) REVERT: M 314 ASN cc_start: 0.7610 (t0) cc_final: 0.7264 (t0) REVERT: M 478 LYS cc_start: 0.8091 (tppt) cc_final: 0.7505 (ttmt) REVERT: M 481 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6747 (tm-30) REVERT: M 494 GLN cc_start: 0.7471 (mt0) cc_final: 0.7219 (mt0) REVERT: M 521 GLN cc_start: 0.7666 (tt0) cc_final: 0.7360 (tt0) REVERT: M 523 ASN cc_start: 0.7890 (p0) cc_final: 0.7628 (p0) REVERT: N 129 ARG cc_start: 0.6690 (mmt90) cc_final: 0.6483 (mmt180) REVERT: N 163 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7218 (mttp) REVERT: N 289 ARG cc_start: 0.6213 (ttp-170) cc_final: 0.5277 (mmm160) REVERT: N 441 GLN cc_start: 0.5860 (mp10) cc_final: 0.5445 (mm-40) REVERT: N 517 ASP cc_start: 0.5810 (p0) cc_final: 0.5147 (p0) REVERT: N 525 TYR cc_start: 0.5461 (m-80) cc_final: 0.4775 (m-10) REVERT: N 547 PHE cc_start: 0.7416 (t80) cc_final: 0.7177 (t80) REVERT: N 550 MET cc_start: 0.5993 (mtm) cc_final: 0.5661 (mtm) REVERT: N 571 ARG cc_start: 0.6071 (ptt180) cc_final: 0.5666 (tmt-80) REVERT: Q 95 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8402 (t) REVERT: Q 117 ASP cc_start: 0.7600 (t0) cc_final: 0.7359 (t0) REVERT: Q 161 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7573 (tp-100) REVERT: Q 376 GLN cc_start: 0.7859 (mp10) cc_final: 0.7583 (mp10) REVERT: O 85 GLN cc_start: 0.8774 (tt0) cc_final: 0.8527 (tt0) REVERT: O 87 LEU cc_start: 0.8388 (tp) cc_final: 0.8183 (tp) REVERT: O 254 MET cc_start: 0.8593 (tpp) cc_final: 0.8385 (tpt) REVERT: O 402 MET cc_start: 0.8478 (ttt) cc_final: 0.7979 (ttt) REVERT: O 435 MET cc_start: 0.7336 (tpt) cc_final: 0.6767 (tpt) REVERT: O 497 GLN cc_start: 0.6263 (tp-100) cc_final: 0.6055 (mm110) REVERT: P 61 ASP cc_start: 0.6938 (t70) cc_final: 0.6635 (t0) REVERT: P 141 ARG cc_start: 0.6924 (mtm180) cc_final: 0.6422 (mmm-85) REVERT: P 249 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7188 (mt-10) REVERT: P 300 MET cc_start: 0.8842 (mmm) cc_final: 0.8624 (tpp) REVERT: P 421 GLN cc_start: 0.8297 (tp-100) cc_final: 0.8079 (tp-100) REVERT: P 456 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6388 (mp10) REVERT: P 491 MET cc_start: 0.7287 (mtp) cc_final: 0.7014 (mtp) REVERT: b 141 PHE cc_start: 0.7987 (t80) cc_final: 0.7688 (t80) REVERT: c 59 LYS cc_start: 0.7697 (tptt) cc_final: 0.7391 (tptt) REVERT: c 65 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6371 (tm-30) REVERT: c 201 ASP cc_start: 0.8197 (m-30) cc_final: 0.7950 (m-30) REVERT: c 219 ASN cc_start: 0.7426 (t0) cc_final: 0.7007 (t0) REVERT: g 75 GLN cc_start: 0.5436 (pp30) cc_final: 0.4764 (mm-40) REVERT: g 88 GLN cc_start: 0.6678 (tm-30) cc_final: 0.6383 (tm-30) REVERT: e 93 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6560 (mp0) outliers start: 18 outliers final: 10 residues processed: 785 average time/residue: 0.2510 time to fit residues: 300.6312 Evaluate side-chains 537 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 526 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 365 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 172 ASN L 231 GLN L 441 GLN D 91 GLN D 137 ASN D 152 GLN U 145 GLN U 257 GLN ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN U 434 GLN d 100 GLN d 139 GLN M 65 GLN M 123 ASN M 314 ASN M 430 GLN M 468 HIS M 494 GLN N 65 GLN N 242 GLN N 268 ASN N 430 GLN N 449 ASN N 494 GLN N 573 HIS Q 97 GLN Q 181 ASN Q 199 HIS Q 256 ASN ** Q 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 199 HIS O 262 ASN O 292 HIS O 385 ASN O 433 GLN O 456 GLN P 199 HIS P 256 ASN P 421 GLN b 71 GLN b 78 GLN b 206 GLN c 113 GLN g 89 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116604 restraints weight = 59755.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115582 restraints weight = 50873.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116297 restraints weight = 44825.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116980 restraints weight = 37137.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117100 restraints weight = 30888.467| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36854 Z= 0.142 Angle : 0.616 13.855 49840 Z= 0.327 Chirality : 0.045 0.253 5616 Planarity : 0.006 0.067 6505 Dihedral : 5.961 72.296 5104 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.04 % Allowed : 13.92 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -4.12 (0.10), residues: 4623 helix: -3.09 (0.09), residues: 1956 sheet: -1.99 (0.20), residues: 619 loop : -2.44 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG g 79 TYR 0.015 0.001 TYR Q 303 PHE 0.019 0.001 PHE L 612 TRP 0.018 0.001 TRP L 450 HIS 0.010 0.001 HIS d 14 Details of bonding type rmsd covalent geometry : bond 0.00315 (36854) covalent geometry : angle 0.61585 (49840) hydrogen bonds : bond 0.05068 ( 1199) hydrogen bonds : angle 5.81010 ( 3435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 580 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: L 200 LYS cc_start: 0.6003 (ttmt) cc_final: 0.5392 (pttm) REVERT: L 235 ASP cc_start: 0.7986 (m-30) cc_final: 0.7637 (m-30) REVERT: L 458 MET cc_start: 0.7602 (mtt) cc_final: 0.7276 (mtt) REVERT: L 484 GLN cc_start: 0.5951 (tp-100) cc_final: 0.5625 (tp40) REVERT: L 486 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6853 (tt0) REVERT: L 516 LYS cc_start: 0.7194 (mttt) cc_final: 0.6982 (mttt) REVERT: L 544 MET cc_start: 0.6426 (mtt) cc_final: 0.6166 (mtt) REVERT: L 574 MET cc_start: 0.4519 (mtm) cc_final: 0.4232 (mtm) REVERT: D 10 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6267 (m-80) REVERT: D 34 LYS cc_start: 0.7356 (tptm) cc_final: 0.6964 (tttp) REVERT: D 56 MET cc_start: 0.4863 (mmt) cc_final: 0.4418 (ppp) REVERT: D 214 GLU cc_start: 0.5402 (mt-10) cc_final: 0.5129 (tp30) REVERT: U 72 ARG cc_start: 0.3147 (mtt90) cc_final: 0.2890 (ttm110) REVERT: U 111 MET cc_start: 0.5442 (mtm) cc_final: 0.5192 (mtt) REVERT: U 124 ARG cc_start: 0.5926 (ttt180) cc_final: 0.5550 (ttt-90) REVERT: U 173 MET cc_start: 0.3314 (mmt) cc_final: 0.2705 (mmt) REVERT: U 199 TRP cc_start: 0.6319 (t60) cc_final: 0.6027 (t60) REVERT: U 243 GLU cc_start: 0.3995 (pp20) cc_final: 0.3541 (mt-10) REVERT: d 20 GLU cc_start: 0.5351 (mm-30) cc_final: 0.5088 (mm-30) REVERT: d 47 GLN cc_start: 0.6717 (mp10) cc_final: 0.6392 (mp10) REVERT: d 70 ILE cc_start: 0.8074 (mm) cc_final: 0.7724 (mt) REVERT: d 111 ARG cc_start: 0.6556 (ttp-110) cc_final: 0.5914 (mtp180) REVERT: M 314 ASN cc_start: 0.7622 (t0) cc_final: 0.7091 (t0) REVERT: M 334 SER cc_start: 0.8869 (p) cc_final: 0.8654 (m) REVERT: M 344 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7907 (t) REVERT: M 478 LYS cc_start: 0.8218 (tppt) cc_final: 0.7849 (ttmt) REVERT: M 494 GLN cc_start: 0.7761 (mt0) cc_final: 0.7553 (mt0) REVERT: M 513 LYS cc_start: 0.8189 (tmtt) cc_final: 0.7278 (ttmt) REVERT: M 523 ASN cc_start: 0.7862 (p0) cc_final: 0.7507 (p0) REVERT: N 163 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7262 (mttp) REVERT: N 289 ARG cc_start: 0.6262 (ttp-170) cc_final: 0.5986 (ttp-170) REVERT: N 515 ILE cc_start: 0.6401 (mt) cc_final: 0.6129 (mm) REVERT: N 525 TYR cc_start: 0.5387 (m-80) cc_final: 0.4328 (p90) REVERT: N 547 PHE cc_start: 0.7222 (t80) cc_final: 0.6934 (t80) REVERT: N 571 ARG cc_start: 0.6226 (ptt180) cc_final: 0.5911 (tmt-80) REVERT: Q 161 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7671 (tp40) REVERT: Q 249 GLU cc_start: 0.6068 (pt0) cc_final: 0.5839 (mt-10) REVERT: Q 269 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8059 (mm) REVERT: Q 421 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8477 (tp-100) REVERT: Q 446 SER cc_start: 0.7620 (m) cc_final: 0.7275 (p) REVERT: Q 460 ARG cc_start: 0.7380 (mmt180) cc_final: 0.6616 (mtp-110) REVERT: O 87 LEU cc_start: 0.8690 (tp) cc_final: 0.8486 (tp) REVERT: O 88 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7596 (tm-30) REVERT: O 402 MET cc_start: 0.8353 (ttt) cc_final: 0.7866 (ttt) REVERT: P 61 ASP cc_start: 0.7169 (t70) cc_final: 0.6940 (t0) REVERT: P 141 ARG cc_start: 0.6899 (mtm180) cc_final: 0.6400 (mmm-85) REVERT: P 300 MET cc_start: 0.8943 (mmm) cc_final: 0.8719 (tpp) REVERT: P 402 MET cc_start: 0.8093 (ttt) cc_final: 0.7806 (ttp) REVERT: P 456 GLN cc_start: 0.7086 (mm-40) cc_final: 0.5839 (mp10) REVERT: b 141 PHE cc_start: 0.7931 (t80) cc_final: 0.7693 (t80) REVERT: c 59 LYS cc_start: 0.7514 (tptt) cc_final: 0.7282 (tptt) REVERT: c 219 ASN cc_start: 0.7446 (t0) cc_final: 0.7167 (t0) REVERT: g 88 GLN cc_start: 0.6423 (tm-30) cc_final: 0.6219 (tm-30) REVERT: g 104 CYS cc_start: 0.7213 (m) cc_final: 0.6969 (p) REVERT: e 93 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6431 (mp0) REVERT: e 110 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7491 (p) outliers start: 79 outliers final: 37 residues processed: 631 average time/residue: 0.2243 time to fit residues: 225.5485 Evaluate side-chains 547 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 506 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 517 ASP Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 268 ASN Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 269 ILE Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 284 optimal weight: 6.9990 chunk 390 optimal weight: 7.9990 chunk 422 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 428 optimal weight: 5.9990 chunk 402 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 415 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN L 449 ASN U 85 ASN ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 221 ASN N 164 HIS N 494 GLN Q 433 GLN O 205 GLN P 415 HIS P 421 GLN ** c 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112091 restraints weight = 60398.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110871 restraints weight = 52960.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111692 restraints weight = 44103.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112157 restraints weight = 38175.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112336 restraints weight = 31701.993| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 36854 Z= 0.288 Angle : 0.730 15.451 49840 Z= 0.377 Chirality : 0.050 0.238 5616 Planarity : 0.006 0.073 6505 Dihedral : 6.138 75.473 5093 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.70 % Allowed : 16.84 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -3.70 (0.11), residues: 4623 helix: -2.48 (0.10), residues: 1949 sheet: -2.09 (0.20), residues: 615 loop : -2.41 (0.12), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 232 TYR 0.024 0.002 TYR c 112 PHE 0.023 0.002 PHE M 469 TRP 0.019 0.002 TRP L 450 HIS 0.010 0.001 HIS U 445 Details of bonding type rmsd covalent geometry : bond 0.00690 (36854) covalent geometry : angle 0.72952 (49840) hydrogen bonds : bond 0.05032 ( 1199) hydrogen bonds : angle 5.59354 ( 3435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 516 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: L 200 LYS cc_start: 0.6157 (ttmt) cc_final: 0.5672 (pttm) REVERT: L 235 ASP cc_start: 0.8092 (m-30) cc_final: 0.7734 (m-30) REVERT: L 458 MET cc_start: 0.7589 (mtt) cc_final: 0.7333 (mtt) REVERT: L 484 GLN cc_start: 0.6062 (tp-100) cc_final: 0.5712 (tp40) REVERT: L 516 LYS cc_start: 0.7192 (mttt) cc_final: 0.6940 (mttt) REVERT: L 544 MET cc_start: 0.6516 (mtt) cc_final: 0.6263 (mtt) REVERT: L 579 TYR cc_start: 0.7013 (t80) cc_final: 0.6560 (t80) REVERT: D 10 PHE cc_start: 0.6793 (t80) cc_final: 0.6283 (m-80) REVERT: D 34 LYS cc_start: 0.7481 (tptm) cc_final: 0.7073 (tttp) REVERT: D 62 MET cc_start: 0.5138 (mtt) cc_final: 0.4618 (mmm) REVERT: U 72 ARG cc_start: 0.3421 (mtt90) cc_final: 0.3164 (ttm110) REVERT: U 104 GLU cc_start: 0.2938 (mt-10) cc_final: 0.2115 (mm-30) REVERT: U 124 ARG cc_start: 0.5983 (ttt180) cc_final: 0.5600 (ttt-90) REVERT: U 173 MET cc_start: 0.3450 (mmt) cc_final: 0.2739 (mmt) REVERT: U 199 TRP cc_start: 0.6480 (t60) cc_final: 0.5981 (t60) REVERT: U 243 GLU cc_start: 0.3592 (pp20) cc_final: 0.3180 (mt-10) REVERT: U 253 TYR cc_start: 0.7063 (t80) cc_final: 0.6811 (t80) REVERT: U 333 MET cc_start: 0.7689 (mtt) cc_final: 0.7414 (mtt) REVERT: d 20 GLU cc_start: 0.5460 (mm-30) cc_final: 0.5129 (mm-30) REVERT: d 47 GLN cc_start: 0.6820 (mp10) cc_final: 0.6552 (mp10) REVERT: d 68 LYS cc_start: 0.6737 (mttm) cc_final: 0.6312 (tttm) REVERT: d 70 ILE cc_start: 0.8228 (mm) cc_final: 0.7928 (mt) REVERT: d 111 ARG cc_start: 0.6644 (ttp-110) cc_final: 0.6112 (mtp180) REVERT: M 314 ASN cc_start: 0.7864 (t0) cc_final: 0.7489 (t0) REVERT: M 494 GLN cc_start: 0.7895 (mt0) cc_final: 0.7561 (mt0) REVERT: M 505 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7174 (t70) REVERT: M 523 ASN cc_start: 0.8018 (p0) cc_final: 0.7564 (p0) REVERT: N 163 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7240 (mttp) REVERT: N 289 ARG cc_start: 0.6285 (ttp-170) cc_final: 0.5986 (ttp-170) REVERT: N 515 ILE cc_start: 0.6495 (mt) cc_final: 0.6254 (mm) REVERT: N 547 PHE cc_start: 0.7133 (t80) cc_final: 0.6871 (t80) REVERT: N 571 ARG cc_start: 0.6043 (ptt180) cc_final: 0.5734 (tmt-80) REVERT: Q 161 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7691 (tp-100) REVERT: Q 269 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8206 (mt) REVERT: Q 360 ASP cc_start: 0.7210 (p0) cc_final: 0.6793 (p0) REVERT: Q 446 SER cc_start: 0.7732 (m) cc_final: 0.7405 (p) REVERT: Q 460 ARG cc_start: 0.7430 (mmt180) cc_final: 0.6688 (mtp-110) REVERT: O 88 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7995 (tp30) REVERT: O 395 LEU cc_start: 0.8268 (mt) cc_final: 0.8035 (mp) REVERT: P 61 ASP cc_start: 0.7204 (t70) cc_final: 0.6931 (t0) REVERT: P 402 MET cc_start: 0.8253 (ttt) cc_final: 0.7937 (ttp) REVERT: P 456 GLN cc_start: 0.7282 (mm-40) cc_final: 0.6525 (mp10) REVERT: c 93 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: c 100 GLN cc_start: 0.8136 (pt0) cc_final: 0.7805 (mt0) REVERT: c 197 GLU cc_start: 0.8071 (mp0) cc_final: 0.7518 (mt-10) REVERT: c 219 ASN cc_start: 0.7589 (t0) cc_final: 0.7301 (t0) REVERT: g 88 GLN cc_start: 0.6645 (tm-30) cc_final: 0.6443 (tm-30) REVERT: g 89 GLN cc_start: 0.6095 (OUTLIER) cc_final: 0.5879 (mp10) REVERT: e 82 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7423 (mm-40) REVERT: e 93 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6430 (mp0) REVERT: e 109 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6374 (tt0) outliers start: 143 outliers final: 102 residues processed: 618 average time/residue: 0.2192 time to fit residues: 217.5980 Evaluate side-chains 572 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 465 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 485 GLU Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain L residue 584 MET Chi-restraints excluded: chain L residue 592 ASP Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain U residue 31 LEU Chi-restraints excluded: chain U residue 62 MET Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 282 LEU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 284 MET Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 505 ASP Chi-restraints excluded: chain M residue 517 ASP Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 493 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 269 ILE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 177 ILE Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain g residue 89 GLN Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 109 GLN Chi-restraints excluded: chain f residue 102 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 219 optimal weight: 6.9990 chunk 416 optimal weight: 3.9990 chunk 361 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 409 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 382 optimal weight: 0.9980 chunk 368 optimal weight: 3.9990 chunk 348 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN ** U 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 163 GLN U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN M 494 GLN N 268 ASN O 363 HIS b 71 GLN c 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114560 restraints weight = 59910.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113463 restraints weight = 53965.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114099 restraints weight = 45543.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114437 restraints weight = 40405.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114712 restraints weight = 34335.350| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36854 Z= 0.170 Angle : 0.603 15.849 49840 Z= 0.313 Chirality : 0.046 0.260 5616 Planarity : 0.004 0.063 6505 Dihedral : 5.664 75.000 5093 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.44 % Allowed : 19.06 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -3.14 (0.11), residues: 4623 helix: -1.91 (0.11), residues: 1942 sheet: -1.88 (0.20), residues: 606 loop : -2.22 (0.12), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 141 TYR 0.030 0.002 TYR c 112 PHE 0.018 0.001 PHE M 469 TRP 0.015 0.001 TRP U 186 HIS 0.008 0.001 HIS U 97 Details of bonding type rmsd covalent geometry : bond 0.00403 (36854) covalent geometry : angle 0.60256 (49840) hydrogen bonds : bond 0.04065 ( 1199) hydrogen bonds : angle 5.16496 ( 3435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 498 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: L 200 LYS cc_start: 0.6114 (ttmt) cc_final: 0.5534 (pttm) REVERT: L 235 ASP cc_start: 0.8092 (m-30) cc_final: 0.7723 (m-30) REVERT: L 284 MET cc_start: 0.6854 (tpp) cc_final: 0.6586 (tpp) REVERT: L 458 MET cc_start: 0.7481 (mtt) cc_final: 0.7257 (mtt) REVERT: L 484 GLN cc_start: 0.6181 (tp-100) cc_final: 0.5838 (tp40) REVERT: L 516 LYS cc_start: 0.7161 (mttt) cc_final: 0.6923 (mttt) REVERT: L 540 MET cc_start: 0.8170 (mtp) cc_final: 0.7786 (mtp) REVERT: L 544 MET cc_start: 0.6444 (mtt) cc_final: 0.6073 (mtt) REVERT: L 579 TYR cc_start: 0.6971 (t80) cc_final: 0.6562 (t80) REVERT: L 596 LYS cc_start: 0.6631 (mtmm) cc_final: 0.6036 (tptp) REVERT: D 10 PHE cc_start: 0.6592 (t80) cc_final: 0.6133 (m-80) REVERT: D 34 LYS cc_start: 0.7457 (tptm) cc_final: 0.6801 (ttmm) REVERT: D 57 LEU cc_start: 0.4257 (OUTLIER) cc_final: 0.4055 (mp) REVERT: D 62 MET cc_start: 0.5220 (mtt) cc_final: 0.4743 (mmm) REVERT: D 138 TYR cc_start: 0.4213 (OUTLIER) cc_final: 0.3832 (m-10) REVERT: U 124 ARG cc_start: 0.6026 (ttt180) cc_final: 0.5665 (ttt-90) REVERT: U 173 MET cc_start: 0.3449 (mmt) cc_final: 0.2998 (mmt) REVERT: U 199 TRP cc_start: 0.6529 (t60) cc_final: 0.6104 (t60) REVERT: U 243 GLU cc_start: 0.3614 (pp20) cc_final: 0.3266 (mt-10) REVERT: U 253 TYR cc_start: 0.6987 (t80) cc_final: 0.6743 (t80) REVERT: U 333 MET cc_start: 0.7648 (mtt) cc_final: 0.7406 (mtt) REVERT: U 432 GLU cc_start: 0.6285 (mp0) cc_final: 0.5879 (mp0) REVERT: d 20 GLU cc_start: 0.5326 (mm-30) cc_final: 0.5057 (mm-30) REVERT: d 47 GLN cc_start: 0.6712 (mp10) cc_final: 0.6447 (mp10) REVERT: d 68 LYS cc_start: 0.6698 (mttm) cc_final: 0.6327 (tttm) REVERT: d 70 ILE cc_start: 0.8182 (mm) cc_final: 0.7840 (mt) REVERT: d 111 ARG cc_start: 0.6646 (ttp-110) cc_final: 0.6066 (mtp180) REVERT: M 74 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8398 (p) REVERT: M 314 ASN cc_start: 0.7800 (t0) cc_final: 0.7413 (t0) REVERT: M 426 LEU cc_start: 0.8504 (mm) cc_final: 0.8168 (mp) REVERT: M 478 LYS cc_start: 0.8365 (tppt) cc_final: 0.7923 (ttmt) REVERT: M 494 GLN cc_start: 0.7819 (mt0) cc_final: 0.7533 (tt0) REVERT: M 505 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7127 (t70) REVERT: M 523 ASN cc_start: 0.8030 (p0) cc_final: 0.7597 (p0) REVERT: N 163 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7177 (mttp) REVERT: N 289 ARG cc_start: 0.6294 (ttp-170) cc_final: 0.5980 (ttp-170) REVERT: N 515 ILE cc_start: 0.6470 (mt) cc_final: 0.6215 (mm) REVERT: N 547 PHE cc_start: 0.7106 (t80) cc_final: 0.6739 (t80) REVERT: N 550 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6180 (mtp) REVERT: Q 161 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7631 (tp-100) REVERT: Q 269 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8176 (mm) REVERT: O 88 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7713 (tm-30) REVERT: P 61 ASP cc_start: 0.7192 (t70) cc_final: 0.6951 (t0) REVERT: P 247 ASP cc_start: 0.7856 (t70) cc_final: 0.7450 (t0) REVERT: P 376 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: P 410 MET cc_start: 0.6602 (mtt) cc_final: 0.6330 (mtm) REVERT: P 456 GLN cc_start: 0.7311 (mm-40) cc_final: 0.6537 (mp10) REVERT: b 111 ARG cc_start: 0.7488 (mtp180) cc_final: 0.7239 (mtp-110) REVERT: c 93 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7176 (m-30) REVERT: c 100 GLN cc_start: 0.8132 (pt0) cc_final: 0.7723 (mt0) REVERT: c 197 GLU cc_start: 0.7912 (mp0) cc_final: 0.7465 (mt-10) REVERT: c 219 ASN cc_start: 0.7598 (t0) cc_final: 0.7306 (t0) REVERT: g 88 GLN cc_start: 0.6684 (tm-30) cc_final: 0.6333 (tm-30) REVERT: e 82 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7405 (mm-40) REVERT: e 93 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6495 (mp0) REVERT: e 109 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.6421 (tt0) outliers start: 133 outliers final: 93 residues processed: 592 average time/residue: 0.2173 time to fit residues: 206.8328 Evaluate side-chains 574 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 472 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain L residue 584 MET Chi-restraints excluded: chain L residue 592 ASP Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 284 MET Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 505 ASP Chi-restraints excluded: chain M residue 517 ASP Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 493 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 269 ILE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 371 TYR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 376 GLN Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 144 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 109 GLN Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 139 optimal weight: 5.9990 chunk 360 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 353 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN d 126 GLN Q 62 HIS O 456 GLN c 77 ASN f 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115919 restraints weight = 59275.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114774 restraints weight = 52905.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115479 restraints weight = 45570.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116087 restraints weight = 37203.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116226 restraints weight = 30963.185| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36854 Z= 0.133 Angle : 0.562 15.670 49840 Z= 0.290 Chirality : 0.044 0.263 5616 Planarity : 0.004 0.070 6505 Dihedral : 5.311 74.672 5093 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.62 % Allowed : 19.32 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.69 (0.11), residues: 4623 helix: -1.43 (0.11), residues: 1945 sheet: -1.70 (0.21), residues: 608 loop : -2.06 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 400 TYR 0.020 0.001 TYR P 423 PHE 0.015 0.001 PHE M 469 TRP 0.012 0.001 TRP U 186 HIS 0.011 0.001 HIS Q 62 Details of bonding type rmsd covalent geometry : bond 0.00310 (36854) covalent geometry : angle 0.56208 (49840) hydrogen bonds : bond 0.03624 ( 1199) hydrogen bonds : angle 4.88302 ( 3435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 513 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: L 200 LYS cc_start: 0.6071 (ttmt) cc_final: 0.5524 (pttm) REVERT: L 235 ASP cc_start: 0.8073 (m-30) cc_final: 0.7746 (m-30) REVERT: L 484 GLN cc_start: 0.6214 (tp-100) cc_final: 0.5723 (tp40) REVERT: L 516 LYS cc_start: 0.7111 (mttt) cc_final: 0.6905 (mttt) REVERT: L 540 MET cc_start: 0.8154 (mtp) cc_final: 0.7739 (mtp) REVERT: L 544 MET cc_start: 0.6442 (mtt) cc_final: 0.6080 (mtt) REVERT: L 579 TYR cc_start: 0.6909 (t80) cc_final: 0.6550 (t80) REVERT: L 596 LYS cc_start: 0.6595 (mtmm) cc_final: 0.6015 (tptp) REVERT: D 10 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: D 46 GLN cc_start: 0.6405 (mp10) cc_final: 0.6139 (mp10) REVERT: D 56 MET cc_start: 0.5944 (ppp) cc_final: 0.5686 (tmm) REVERT: D 62 MET cc_start: 0.5144 (mtt) cc_final: 0.4741 (mmm) REVERT: U 95 MET cc_start: 0.3904 (mmp) cc_final: 0.2094 (ptp) REVERT: U 124 ARG cc_start: 0.6005 (ttt180) cc_final: 0.5628 (ttt-90) REVERT: U 173 MET cc_start: 0.3357 (mmt) cc_final: 0.2876 (mmt) REVERT: U 199 TRP cc_start: 0.6563 (t60) cc_final: 0.6100 (t60) REVERT: U 243 GLU cc_start: 0.3572 (pp20) cc_final: 0.3098 (mt-10) REVERT: U 273 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6966 (mt-10) REVERT: U 432 GLU cc_start: 0.6280 (mp0) cc_final: 0.5826 (mp0) REVERT: d 8 VAL cc_start: 0.6002 (OUTLIER) cc_final: 0.5708 (t) REVERT: d 20 GLU cc_start: 0.5298 (mm-30) cc_final: 0.5032 (mm-30) REVERT: d 47 GLN cc_start: 0.6713 (mp10) cc_final: 0.6426 (mp10) REVERT: d 68 LYS cc_start: 0.6695 (mttm) cc_final: 0.6360 (tttm) REVERT: d 111 ARG cc_start: 0.6635 (ttp-110) cc_final: 0.6107 (mtp180) REVERT: M 74 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8450 (p) REVERT: M 314 ASN cc_start: 0.7779 (t0) cc_final: 0.7432 (t0) REVERT: M 426 LEU cc_start: 0.8532 (mm) cc_final: 0.8284 (mp) REVERT: M 478 LYS cc_start: 0.8333 (tppt) cc_final: 0.7785 (ttmt) REVERT: M 494 GLN cc_start: 0.7848 (mt0) cc_final: 0.7578 (tt0) REVERT: M 505 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.7119 (t70) REVERT: M 523 ASN cc_start: 0.7988 (p0) cc_final: 0.7599 (p0) REVERT: N 163 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7392 (mttp) REVERT: N 268 ASN cc_start: 0.6439 (OUTLIER) cc_final: 0.6229 (t0) REVERT: N 289 ARG cc_start: 0.6271 (ttp-170) cc_final: 0.5942 (ttp-170) REVERT: N 547 PHE cc_start: 0.7085 (t80) cc_final: 0.6664 (t80) REVERT: N 550 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6382 (mtp) REVERT: Q 161 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7620 (tp-100) REVERT: Q 421 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8390 (tp-100) REVERT: O 88 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7718 (tm-30) REVERT: O 435 MET cc_start: 0.7672 (tpt) cc_final: 0.7245 (tpp) REVERT: P 127 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7109 (mtm) REVERT: P 247 ASP cc_start: 0.7890 (t70) cc_final: 0.7460 (t0) REVERT: P 456 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6565 (mp10) REVERT: b 111 ARG cc_start: 0.7453 (mtp180) cc_final: 0.7204 (mtp-110) REVERT: c 100 GLN cc_start: 0.8087 (pt0) cc_final: 0.7655 (mt0) REVERT: c 197 GLU cc_start: 0.7872 (mp0) cc_final: 0.7479 (mt-10) REVERT: c 219 ASN cc_start: 0.7695 (t0) cc_final: 0.7457 (t0) REVERT: g 88 GLN cc_start: 0.6754 (tm-30) cc_final: 0.6365 (tm-30) REVERT: e 82 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7315 (mm-40) REVERT: e 93 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6543 (mp0) outliers start: 140 outliers final: 91 residues processed: 609 average time/residue: 0.2154 time to fit residues: 212.3543 Evaluate side-chains 577 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 478 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 346 MET Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain L residue 584 MET Chi-restraints excluded: chain D residue 10 PHE Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 273 GLU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 58 GLU Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 505 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 268 ASN Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 493 VAL Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 371 TYR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 427 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 333 optimal weight: 7.9990 chunk 361 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 433 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 152 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114255 restraints weight = 59958.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113069 restraints weight = 55036.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113833 restraints weight = 46819.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114562 restraints weight = 38077.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114612 restraints weight = 33725.327| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 36854 Z= 0.207 Angle : 0.621 15.962 49840 Z= 0.321 Chirality : 0.047 0.254 5616 Planarity : 0.005 0.067 6505 Dihedral : 5.514 75.450 5093 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.16 % Allowed : 19.79 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.64 (0.11), residues: 4623 helix: -1.35 (0.11), residues: 1952 sheet: -1.76 (0.20), residues: 608 loop : -2.05 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 442 TYR 0.029 0.002 TYR c 112 PHE 0.018 0.002 PHE M 469 TRP 0.014 0.002 TRP L 450 HIS 0.007 0.001 HIS U 445 Details of bonding type rmsd covalent geometry : bond 0.00496 (36854) covalent geometry : angle 0.62136 (49840) hydrogen bonds : bond 0.03862 ( 1199) hydrogen bonds : angle 4.98095 ( 3435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 484 time to evaluate : 1.273 Fit side-chains REVERT: L 200 LYS cc_start: 0.6072 (ttmt) cc_final: 0.5511 (pttm) REVERT: L 235 ASP cc_start: 0.8081 (m-30) cc_final: 0.7705 (m-30) REVERT: L 484 GLN cc_start: 0.6219 (tp-100) cc_final: 0.5730 (tp40) REVERT: L 540 MET cc_start: 0.8210 (mtp) cc_final: 0.7939 (mtp) REVERT: L 544 MET cc_start: 0.6417 (mtt) cc_final: 0.6052 (mtt) REVERT: L 556 GLU cc_start: 0.5388 (OUTLIER) cc_final: 0.4095 (tm-30) REVERT: L 579 TYR cc_start: 0.7032 (t80) cc_final: 0.6589 (t80) REVERT: L 596 LYS cc_start: 0.6682 (mtmm) cc_final: 0.6037 (tptp) REVERT: D 10 PHE cc_start: 0.6484 (t80) cc_final: 0.6014 (m-80) REVERT: D 56 MET cc_start: 0.5969 (ppp) cc_final: 0.5765 (tmm) REVERT: D 62 MET cc_start: 0.5258 (mtt) cc_final: 0.4891 (mmm) REVERT: D 138 TYR cc_start: 0.4224 (OUTLIER) cc_final: 0.4018 (m-10) REVERT: U 95 MET cc_start: 0.3971 (mmp) cc_final: 0.2022 (ttp) REVERT: U 109 MET cc_start: 0.4677 (mmt) cc_final: 0.3867 (mmm) REVERT: U 124 ARG cc_start: 0.6038 (ttt180) cc_final: 0.5658 (ttt-90) REVERT: U 173 MET cc_start: 0.3490 (mmt) cc_final: 0.2637 (mmt) REVERT: U 199 TRP cc_start: 0.6594 (t60) cc_final: 0.5869 (t60) REVERT: U 273 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: U 333 MET cc_start: 0.7649 (mtt) cc_final: 0.7316 (mtt) REVERT: d 8 VAL cc_start: 0.5997 (OUTLIER) cc_final: 0.5703 (t) REVERT: d 20 GLU cc_start: 0.5279 (mm-30) cc_final: 0.5014 (mm-30) REVERT: d 47 GLN cc_start: 0.6693 (mp10) cc_final: 0.6402 (mp10) REVERT: d 57 TYR cc_start: 0.6980 (m-80) cc_final: 0.6540 (m-10) REVERT: d 68 LYS cc_start: 0.6796 (mttm) cc_final: 0.6406 (tttm) REVERT: d 111 ARG cc_start: 0.6572 (ttp-110) cc_final: 0.6088 (mtp180) REVERT: d 139 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: M 74 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8418 (p) REVERT: M 314 ASN cc_start: 0.7863 (t0) cc_final: 0.7494 (t0) REVERT: M 426 LEU cc_start: 0.8573 (mm) cc_final: 0.8225 (mp) REVERT: M 494 GLN cc_start: 0.7856 (mt0) cc_final: 0.7595 (tt0) REVERT: M 523 ASN cc_start: 0.8122 (p0) cc_final: 0.7688 (p0) REVERT: N 163 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7171 (mttp) REVERT: N 289 ARG cc_start: 0.6211 (ttp-170) cc_final: 0.5964 (ttp-170) REVERT: N 450 TRP cc_start: 0.7154 (p90) cc_final: 0.6906 (p90) REVERT: N 550 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6089 (mtp) REVERT: N 597 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6106 (mp) REVERT: Q 161 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7794 (tp-100) REVERT: O 88 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7776 (tm-30) REVERT: O 435 MET cc_start: 0.7655 (tpt) cc_final: 0.7355 (tpt) REVERT: P 247 ASP cc_start: 0.7859 (t70) cc_final: 0.7434 (t0) REVERT: P 376 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: P 456 GLN cc_start: 0.7373 (mm-40) cc_final: 0.6590 (mp10) REVERT: b 111 ARG cc_start: 0.7510 (mtp180) cc_final: 0.7228 (mtp-110) REVERT: c 100 GLN cc_start: 0.8031 (pt0) cc_final: 0.7649 (mt0) REVERT: c 197 GLU cc_start: 0.7881 (mp0) cc_final: 0.7497 (mt-10) REVERT: c 219 ASN cc_start: 0.7669 (t0) cc_final: 0.7416 (t0) REVERT: g 88 GLN cc_start: 0.6774 (tm-30) cc_final: 0.6464 (tm-30) REVERT: e 93 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6605 (mp0) outliers start: 161 outliers final: 122 residues processed: 615 average time/residue: 0.2108 time to fit residues: 210.8380 Evaluate side-chains 600 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 469 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 273 GLU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 452 VAL Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 105 VAL Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 150 LYS Chi-restraints excluded: chain d residue 168 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 493 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 597 ILE Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 371 TYR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 376 GLN Chi-restraints excluded: chain P residue 403 LYS Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 144 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 152 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain g residue 89 GLN Chi-restraints excluded: chain g residue 96 LEU Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 155 optimal weight: 0.0010 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 409 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 425 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN L 573 HIS U 319 GLN U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN N 268 ASN P 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115137 restraints weight = 59637.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114847 restraints weight = 52696.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115269 restraints weight = 47867.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116159 restraints weight = 40505.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116166 restraints weight = 34308.841| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36854 Z= 0.121 Angle : 0.553 17.233 49840 Z= 0.286 Chirality : 0.044 0.248 5616 Planarity : 0.004 0.076 6505 Dihedral : 5.151 74.934 5093 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.41 % Allowed : 20.74 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.23 (0.12), residues: 4623 helix: -0.94 (0.12), residues: 1946 sheet: -1.63 (0.20), residues: 615 loop : -1.86 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 72 TYR 0.044 0.001 TYR c 112 PHE 0.014 0.001 PHE D 199 TRP 0.016 0.001 TRP U 186 HIS 0.005 0.001 HIS U 97 Details of bonding type rmsd covalent geometry : bond 0.00282 (36854) covalent geometry : angle 0.55329 (49840) hydrogen bonds : bond 0.03385 ( 1199) hydrogen bonds : angle 4.73273 ( 3435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 497 time to evaluate : 1.234 Fit side-chains REVERT: L 200 LYS cc_start: 0.5997 (ttmt) cc_final: 0.5609 (pttm) REVERT: L 235 ASP cc_start: 0.8123 (m-30) cc_final: 0.7805 (m-30) REVERT: L 484 GLN cc_start: 0.6262 (tp-100) cc_final: 0.5657 (tp40) REVERT: L 540 MET cc_start: 0.8154 (mtp) cc_final: 0.7740 (mtp) REVERT: L 544 MET cc_start: 0.6382 (mtt) cc_final: 0.6072 (mtt) REVERT: L 579 TYR cc_start: 0.6965 (t80) cc_final: 0.6624 (t80) REVERT: L 596 LYS cc_start: 0.6400 (mtmm) cc_final: 0.5885 (tptp) REVERT: D 10 PHE cc_start: 0.6461 (t80) cc_final: 0.5930 (m-80) REVERT: D 56 MET cc_start: 0.5968 (ppp) cc_final: 0.5764 (tmm) REVERT: D 119 TYR cc_start: 0.3551 (m-80) cc_final: 0.3212 (m-10) REVERT: D 138 TYR cc_start: 0.4252 (OUTLIER) cc_final: 0.4011 (m-10) REVERT: U 95 MET cc_start: 0.3978 (mmp) cc_final: 0.2302 (ptp) REVERT: U 109 MET cc_start: 0.4494 (mmt) cc_final: 0.3691 (mmm) REVERT: U 124 ARG cc_start: 0.6031 (ttt180) cc_final: 0.5669 (ttt-90) REVERT: U 173 MET cc_start: 0.3352 (mmt) cc_final: 0.2819 (mmt) REVERT: U 199 TRP cc_start: 0.6607 (t60) cc_final: 0.5962 (t60) REVERT: U 273 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: d 8 VAL cc_start: 0.6111 (OUTLIER) cc_final: 0.5815 (t) REVERT: d 20 GLU cc_start: 0.5128 (mm-30) cc_final: 0.4885 (mm-30) REVERT: d 37 GLU cc_start: 0.7263 (tp30) cc_final: 0.6876 (tp30) REVERT: d 47 GLN cc_start: 0.6668 (mp10) cc_final: 0.6416 (mp10) REVERT: d 68 LYS cc_start: 0.6792 (mttm) cc_final: 0.6520 (tttm) REVERT: d 111 ARG cc_start: 0.6374 (ttp-110) cc_final: 0.5987 (mtp180) REVERT: d 139 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6952 (tm-30) REVERT: d 194 ASN cc_start: 0.7988 (t0) cc_final: 0.7757 (t0) REVERT: M 74 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8500 (p) REVERT: M 142 ARG cc_start: 0.6422 (ptp90) cc_final: 0.5678 (mtt180) REVERT: M 314 ASN cc_start: 0.7733 (t0) cc_final: 0.7367 (t0) REVERT: M 426 LEU cc_start: 0.8553 (mm) cc_final: 0.8297 (mp) REVERT: M 478 LYS cc_start: 0.8339 (tppt) cc_final: 0.7753 (ttmt) REVERT: M 494 GLN cc_start: 0.7847 (mt0) cc_final: 0.7599 (tt0) REVERT: M 523 ASN cc_start: 0.7991 (p0) cc_final: 0.7617 (p0) REVERT: N 163 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7346 (mttp) REVERT: N 289 ARG cc_start: 0.6205 (ttp-170) cc_final: 0.5978 (ttp-170) REVERT: N 450 TRP cc_start: 0.6998 (p90) cc_final: 0.6778 (p90) REVERT: N 550 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.5977 (mtp) REVERT: Q 161 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7736 (tp-100) REVERT: Q 360 ASP cc_start: 0.7067 (p0) cc_final: 0.6771 (p0) REVERT: Q 421 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8431 (tp-100) REVERT: O 435 MET cc_start: 0.7596 (tpt) cc_final: 0.7261 (tpp) REVERT: O 456 GLN cc_start: 0.7321 (tt0) cc_final: 0.7064 (tp-100) REVERT: P 63 VAL cc_start: 0.8916 (t) cc_final: 0.8599 (m) REVERT: P 247 ASP cc_start: 0.7835 (t70) cc_final: 0.7419 (t0) REVERT: P 456 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6503 (mp10) REVERT: b 111 ARG cc_start: 0.7403 (mtp180) cc_final: 0.7140 (mtp-110) REVERT: b 132 MET cc_start: 0.7674 (mtt) cc_final: 0.7447 (mtt) REVERT: c 197 GLU cc_start: 0.7737 (mp0) cc_final: 0.7432 (mt-10) REVERT: c 201 ASP cc_start: 0.8047 (m-30) cc_final: 0.7814 (m-30) REVERT: c 219 ASN cc_start: 0.7651 (t0) cc_final: 0.7409 (t0) REVERT: g 88 GLN cc_start: 0.6752 (tm-30) cc_final: 0.6359 (tm-30) REVERT: e 82 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7415 (mm-40) REVERT: e 93 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6620 (mp0) outliers start: 132 outliers final: 100 residues processed: 598 average time/residue: 0.2118 time to fit residues: 205.4412 Evaluate side-chains 577 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 471 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 584 MET Chi-restraints excluded: chain D residue 14 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 273 GLU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 452 VAL Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 288 LEU Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 268 ASN Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 421 VAL Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 171 GLN Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 371 TYR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 499 THR Chi-restraints excluded: chain P residue 39 TYR Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain g residue 89 GLN Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 102 MET Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 277 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 347 optimal weight: 5.9990 chunk 307 optimal weight: 0.4980 chunk 226 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 311 optimal weight: 0.8980 chunk 308 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 428 optimal weight: 0.3980 chunk 248 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN N 268 ASN N 484 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116521 restraints weight = 59096.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116037 restraints weight = 54447.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117078 restraints weight = 47805.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117536 restraints weight = 34279.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117589 restraints weight = 30059.052| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36854 Z= 0.113 Angle : 0.545 16.545 49840 Z= 0.281 Chirality : 0.043 0.273 5616 Planarity : 0.004 0.062 6505 Dihedral : 4.944 74.989 5093 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.34 % Allowed : 21.11 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -1.91 (0.12), residues: 4623 helix: -0.62 (0.12), residues: 1952 sheet: -1.51 (0.21), residues: 611 loop : -1.74 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 571 TYR 0.016 0.001 TYR P 423 PHE 0.019 0.001 PHE d 141 TRP 0.020 0.001 TRP M 433 HIS 0.005 0.001 HIS U 97 Details of bonding type rmsd covalent geometry : bond 0.00261 (36854) covalent geometry : angle 0.54500 (49840) hydrogen bonds : bond 0.03189 ( 1199) hydrogen bonds : angle 4.58737 ( 3435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 504 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: L 200 LYS cc_start: 0.5973 (ttmt) cc_final: 0.5572 (pttm) REVERT: L 235 ASP cc_start: 0.8064 (m-30) cc_final: 0.7730 (m-30) REVERT: L 484 GLN cc_start: 0.6254 (tp-100) cc_final: 0.5691 (tp40) REVERT: L 540 MET cc_start: 0.8117 (mtp) cc_final: 0.7878 (mtp) REVERT: L 544 MET cc_start: 0.6361 (mtt) cc_final: 0.6050 (mtt) REVERT: L 556 GLU cc_start: 0.5403 (OUTLIER) cc_final: 0.4972 (tp30) REVERT: L 579 TYR cc_start: 0.7013 (t80) cc_final: 0.6694 (t80) REVERT: L 596 LYS cc_start: 0.6548 (mtmm) cc_final: 0.6008 (tptp) REVERT: D 10 PHE cc_start: 0.6451 (t80) cc_final: 0.5962 (m-80) REVERT: D 62 MET cc_start: 0.4579 (mmm) cc_final: 0.4236 (mmm) REVERT: D 138 TYR cc_start: 0.4078 (OUTLIER) cc_final: 0.3716 (m-10) REVERT: U 95 MET cc_start: 0.3753 (mmp) cc_final: 0.2317 (ptp) REVERT: U 109 MET cc_start: 0.4437 (mmt) cc_final: 0.3693 (mmm) REVERT: U 111 MET cc_start: 0.4854 (mtt) cc_final: 0.4382 (mmm) REVERT: U 124 ARG cc_start: 0.6086 (ttt180) cc_final: 0.5682 (ttt-90) REVERT: U 273 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6791 (mt-10) REVERT: U 432 GLU cc_start: 0.6489 (mp0) cc_final: 0.5990 (mp0) REVERT: d 8 VAL cc_start: 0.6082 (OUTLIER) cc_final: 0.5801 (t) REVERT: d 20 GLU cc_start: 0.5060 (mm-30) cc_final: 0.4840 (mm-30) REVERT: d 37 GLU cc_start: 0.7249 (tp30) cc_final: 0.6863 (tp30) REVERT: d 47 GLN cc_start: 0.6684 (mp10) cc_final: 0.6451 (mp10) REVERT: d 68 LYS cc_start: 0.6796 (mttm) cc_final: 0.6513 (tttm) REVERT: d 111 ARG cc_start: 0.6412 (ttp-110) cc_final: 0.6013 (mtp180) REVERT: d 139 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: d 194 ASN cc_start: 0.7976 (t0) cc_final: 0.7759 (t0) REVERT: M 142 ARG cc_start: 0.6385 (ptp90) cc_final: 0.5660 (mtt180) REVERT: M 314 ASN cc_start: 0.7673 (t0) cc_final: 0.7330 (t0) REVERT: M 426 LEU cc_start: 0.8563 (mm) cc_final: 0.8319 (mp) REVERT: M 478 LYS cc_start: 0.8306 (tppt) cc_final: 0.7782 (ttmt) REVERT: M 494 GLN cc_start: 0.7860 (mt0) cc_final: 0.7646 (tt0) REVERT: M 523 ASN cc_start: 0.7937 (p0) cc_final: 0.7358 (p0) REVERT: N 163 LYS cc_start: 0.7633 (mmtt) cc_final: 0.7373 (mttp) REVERT: N 289 ARG cc_start: 0.6192 (ttp-170) cc_final: 0.5958 (ttp-170) REVERT: N 450 TRP cc_start: 0.6994 (p90) cc_final: 0.6699 (p90) REVERT: N 550 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5727 (mtp) REVERT: N 597 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6224 (mp) REVERT: Q 161 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7742 (tp-100) REVERT: Q 421 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8398 (tp-100) REVERT: P 63 VAL cc_start: 0.8899 (t) cc_final: 0.8579 (m) REVERT: P 127 MET cc_start: 0.7459 (ptp) cc_final: 0.7032 (mtm) REVERT: P 247 ASP cc_start: 0.7873 (t70) cc_final: 0.7464 (t0) REVERT: P 456 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6488 (mp10) REVERT: b 111 ARG cc_start: 0.7403 (mtp180) cc_final: 0.7143 (mtp-110) REVERT: c 197 GLU cc_start: 0.7717 (mp0) cc_final: 0.7419 (mt-10) REVERT: c 219 ASN cc_start: 0.7636 (t0) cc_final: 0.7411 (t0) REVERT: g 88 GLN cc_start: 0.6725 (tm-30) cc_final: 0.6294 (tm-30) REVERT: g 89 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6160 (mp10) REVERT: e 82 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7329 (mm-40) REVERT: e 93 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6694 (mp0) outliers start: 129 outliers final: 102 residues processed: 606 average time/residue: 0.2092 time to fit residues: 205.1460 Evaluate side-chains 583 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 473 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain L residue 584 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 273 GLU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 452 VAL Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 288 LEU Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 597 ILE Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 171 GLN Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 499 THR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 210 GLU Chi-restraints excluded: chain g residue 89 GLN Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 102 MET Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 43 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 411 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 298 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 458 optimal weight: 10.0000 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN N 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114551 restraints weight = 59897.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113799 restraints weight = 58621.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114694 restraints weight = 53411.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115172 restraints weight = 40254.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115431 restraints weight = 34488.475| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36854 Z= 0.197 Angle : 0.619 16.623 49840 Z= 0.318 Chirality : 0.047 0.247 5616 Planarity : 0.005 0.061 6505 Dihedral : 5.280 75.896 5093 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.49 % Allowed : 21.24 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.06 (0.12), residues: 4623 helix: -0.73 (0.12), residues: 1952 sheet: -1.59 (0.20), residues: 615 loop : -1.85 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 353 TYR 0.022 0.002 TYR P 423 PHE 0.020 0.002 PHE M 196 TRP 0.029 0.002 TRP M 433 HIS 0.006 0.001 HIS U 97 Details of bonding type rmsd covalent geometry : bond 0.00472 (36854) covalent geometry : angle 0.61950 (49840) hydrogen bonds : bond 0.03645 ( 1199) hydrogen bonds : angle 4.80388 ( 3435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 471 time to evaluate : 1.100 Fit side-chains REVERT: L 200 LYS cc_start: 0.5977 (ttmt) cc_final: 0.5640 (pttm) REVERT: L 235 ASP cc_start: 0.8093 (m-30) cc_final: 0.7756 (m-30) REVERT: L 387 GLU cc_start: 0.7790 (tp30) cc_final: 0.7520 (tp30) REVERT: L 484 GLN cc_start: 0.6272 (tp-100) cc_final: 0.5671 (tp40) REVERT: L 544 MET cc_start: 0.6434 (mtt) cc_final: 0.6110 (mtt) REVERT: L 556 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.4095 (tm-30) REVERT: L 579 TYR cc_start: 0.7099 (t80) cc_final: 0.6711 (t80) REVERT: L 596 LYS cc_start: 0.6487 (mtmm) cc_final: 0.5968 (tptp) REVERT: D 10 PHE cc_start: 0.6486 (t80) cc_final: 0.6011 (m-80) REVERT: D 62 MET cc_start: 0.4506 (mmm) cc_final: 0.4254 (mmm) REVERT: D 119 TYR cc_start: 0.3802 (m-80) cc_final: 0.3442 (m-10) REVERT: D 138 TYR cc_start: 0.4253 (OUTLIER) cc_final: 0.4003 (m-10) REVERT: U 95 MET cc_start: 0.3789 (mmp) cc_final: 0.2346 (ptp) REVERT: U 111 MET cc_start: 0.4801 (mtt) cc_final: 0.4362 (mmm) REVERT: U 124 ARG cc_start: 0.6005 (ttt180) cc_final: 0.5654 (ttt-90) REVERT: U 199 TRP cc_start: 0.6763 (t60) cc_final: 0.5879 (t60) REVERT: U 261 GLU cc_start: 0.6410 (mp0) cc_final: 0.5458 (mt-10) REVERT: U 273 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: d 8 VAL cc_start: 0.6135 (OUTLIER) cc_final: 0.5818 (t) REVERT: d 20 GLU cc_start: 0.5019 (mm-30) cc_final: 0.4786 (mm-30) REVERT: d 47 GLN cc_start: 0.6657 (mp10) cc_final: 0.6343 (mp10) REVERT: d 68 LYS cc_start: 0.6868 (mttm) cc_final: 0.6544 (tttm) REVERT: d 111 ARG cc_start: 0.6434 (ttp-110) cc_final: 0.6039 (mtp180) REVERT: d 139 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: d 184 TYR cc_start: 0.7331 (m-80) cc_final: 0.7052 (m-80) REVERT: M 142 ARG cc_start: 0.6432 (ptp90) cc_final: 0.5687 (mtt180) REVERT: M 314 ASN cc_start: 0.7846 (t0) cc_final: 0.7490 (t0) REVERT: M 426 LEU cc_start: 0.8568 (mm) cc_final: 0.8210 (mp) REVERT: M 494 GLN cc_start: 0.7917 (mt0) cc_final: 0.7657 (tt0) REVERT: M 523 ASN cc_start: 0.7986 (p0) cc_final: 0.7540 (p0) REVERT: N 163 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7360 (mttp) REVERT: N 450 TRP cc_start: 0.7016 (p90) cc_final: 0.6777 (p90) REVERT: N 550 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5397 (mtp) REVERT: N 597 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6244 (mp) REVERT: Q 161 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7788 (tp-100) REVERT: Q 360 ASP cc_start: 0.7240 (p0) cc_final: 0.6518 (p0) REVERT: P 127 MET cc_start: 0.7506 (ptp) cc_final: 0.7125 (mtm) REVERT: P 247 ASP cc_start: 0.7862 (t70) cc_final: 0.7455 (t0) REVERT: P 376 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: P 456 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6514 (mp10) REVERT: b 111 ARG cc_start: 0.7430 (mtp180) cc_final: 0.7152 (mtp-110) REVERT: c 197 GLU cc_start: 0.7804 (mp0) cc_final: 0.7439 (mt-10) REVERT: c 219 ASN cc_start: 0.7606 (t0) cc_final: 0.7369 (t0) REVERT: g 88 GLN cc_start: 0.6720 (tm-30) cc_final: 0.6370 (tm-30) REVERT: e 82 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7316 (mm-40) REVERT: e 93 GLU cc_start: 0.7621 (mm-30) cc_final: 0.6776 (mp0) outliers start: 135 outliers final: 114 residues processed: 581 average time/residue: 0.2092 time to fit residues: 198.5729 Evaluate side-chains 580 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 458 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 97 HIS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 273 GLU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 391 ASN Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 452 VAL Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 268 ASN Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 358 LEU Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 597 ILE Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 171 GLN Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 499 THR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 376 GLN Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 152 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain c residue 210 GLU Chi-restraints excluded: chain g residue 89 GLN Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 319 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 362 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 406 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 380 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN U 350 HIS ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 ASN Q 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113393 restraints weight = 60024.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112565 restraints weight = 59317.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113326 restraints weight = 54675.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114080 restraints weight = 41348.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114156 restraints weight = 35605.275| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 36854 Z= 0.211 Angle : 0.633 16.542 49840 Z= 0.325 Chirality : 0.047 0.246 5616 Planarity : 0.005 0.062 6505 Dihedral : 5.372 75.735 5092 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.39 % Allowed : 21.42 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.14 (0.12), residues: 4623 helix: -0.79 (0.12), residues: 1962 sheet: -1.65 (0.20), residues: 620 loop : -1.88 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 353 TYR 0.026 0.002 TYR P 423 PHE 0.020 0.002 PHE d 141 TRP 0.037 0.002 TRP M 433 HIS 0.006 0.001 HIS U 97 Details of bonding type rmsd covalent geometry : bond 0.00507 (36854) covalent geometry : angle 0.63288 (49840) hydrogen bonds : bond 0.03700 ( 1199) hydrogen bonds : angle 4.87244 ( 3435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 466 time to evaluate : 1.404 Fit side-chains REVERT: L 200 LYS cc_start: 0.6019 (ttmt) cc_final: 0.5664 (pttm) REVERT: L 235 ASP cc_start: 0.8106 (m-30) cc_final: 0.7718 (m-30) REVERT: L 387 GLU cc_start: 0.7839 (tp30) cc_final: 0.7602 (tp30) REVERT: L 484 GLN cc_start: 0.6282 (tp-100) cc_final: 0.5742 (tp40) REVERT: L 540 MET cc_start: 0.8291 (mtp) cc_final: 0.7979 (mtp) REVERT: L 544 MET cc_start: 0.6359 (mtt) cc_final: 0.6130 (mtt) REVERT: L 556 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4116 (tm-30) REVERT: L 579 TYR cc_start: 0.7104 (t80) cc_final: 0.6695 (t80) REVERT: L 596 LYS cc_start: 0.6537 (mtmm) cc_final: 0.5990 (tptp) REVERT: D 10 PHE cc_start: 0.6517 (t80) cc_final: 0.5920 (m-80) REVERT: D 119 TYR cc_start: 0.3730 (m-80) cc_final: 0.3381 (m-10) REVERT: U 95 MET cc_start: 0.3731 (mmp) cc_final: 0.2294 (ptp) REVERT: U 111 MET cc_start: 0.4837 (mtt) cc_final: 0.4414 (mmm) REVERT: U 124 ARG cc_start: 0.5977 (ttt180) cc_final: 0.5614 (ttt-90) REVERT: U 199 TRP cc_start: 0.6753 (t60) cc_final: 0.6045 (t60) REVERT: U 261 GLU cc_start: 0.6544 (mp0) cc_final: 0.5600 (mt-10) REVERT: U 273 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: U 432 GLU cc_start: 0.6522 (mp0) cc_final: 0.6180 (mp0) REVERT: d 8 VAL cc_start: 0.6153 (OUTLIER) cc_final: 0.5833 (t) REVERT: d 20 GLU cc_start: 0.5036 (mm-30) cc_final: 0.4808 (mm-30) REVERT: d 37 GLU cc_start: 0.7190 (tp30) cc_final: 0.6896 (tp30) REVERT: d 47 GLN cc_start: 0.6700 (mp10) cc_final: 0.6387 (mp10) REVERT: d 68 LYS cc_start: 0.6873 (mttm) cc_final: 0.6564 (tttm) REVERT: d 111 ARG cc_start: 0.6467 (ttp-110) cc_final: 0.6081 (mtp180) REVERT: d 139 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: d 184 TYR cc_start: 0.7324 (m-80) cc_final: 0.7077 (m-80) REVERT: M 142 ARG cc_start: 0.6433 (ptp90) cc_final: 0.5666 (mtt180) REVERT: M 314 ASN cc_start: 0.7841 (t0) cc_final: 0.7493 (t0) REVERT: M 426 LEU cc_start: 0.8581 (mm) cc_final: 0.8291 (mp) REVERT: M 494 GLN cc_start: 0.7892 (mt0) cc_final: 0.7614 (tt0) REVERT: M 523 ASN cc_start: 0.8045 (p0) cc_final: 0.7580 (p0) REVERT: N 550 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5381 (mtp) REVERT: N 597 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.6243 (mp) REVERT: Q 161 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7774 (tp-100) REVERT: Q 254 MET cc_start: 0.7250 (tpt) cc_final: 0.6842 (tpt) REVERT: Q 360 ASP cc_start: 0.7239 (p0) cc_final: 0.6469 (p0) REVERT: P 63 VAL cc_start: 0.8927 (t) cc_final: 0.8629 (m) REVERT: P 247 ASP cc_start: 0.7879 (t70) cc_final: 0.7447 (t0) REVERT: P 376 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: P 456 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6525 (mp10) REVERT: b 111 ARG cc_start: 0.7443 (mtp180) cc_final: 0.7119 (mtp-110) REVERT: c 197 GLU cc_start: 0.7813 (mp0) cc_final: 0.7435 (mt-10) REVERT: c 219 ASN cc_start: 0.7614 (t0) cc_final: 0.7383 (t0) REVERT: g 88 GLN cc_start: 0.6719 (tm-30) cc_final: 0.6341 (tm-30) REVERT: e 82 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7302 (mm-40) REVERT: e 93 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6783 (mp0) outliers start: 131 outliers final: 113 residues processed: 574 average time/residue: 0.2067 time to fit residues: 193.9914 Evaluate side-chains 582 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 462 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 228 LEU Chi-restraints excluded: chain L residue 246 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 295 THR Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 473 VAL Chi-restraints excluded: chain L residue 488 ASP Chi-restraints excluded: chain L residue 492 ILE Chi-restraints excluded: chain L residue 525 TYR Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 99 LEU Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 229 THR Chi-restraints excluded: chain U residue 273 GLU Chi-restraints excluded: chain U residue 314 VAL Chi-restraints excluded: chain U residue 324 CYS Chi-restraints excluded: chain U residue 386 THR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 452 VAL Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 311 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 350 SER Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 371 ASP Chi-restraints excluded: chain M residue 578 LEU Chi-restraints excluded: chain M residue 590 VAL Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 187 THR Chi-restraints excluded: chain N residue 246 THR Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain N residue 452 ILE Chi-restraints excluded: chain N residue 455 SER Chi-restraints excluded: chain N residue 493 VAL Chi-restraints excluded: chain N residue 495 LEU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 555 VAL Chi-restraints excluded: chain N residue 590 VAL Chi-restraints excluded: chain N residue 597 ILE Chi-restraints excluded: chain N residue 598 LYS Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 145 VAL Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 359 ASP Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 433 GLN Chi-restraints excluded: chain Q residue 439 VAL Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 266 ASP Chi-restraints excluded: chain O residue 299 ASP Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain O residue 361 ILE Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 499 THR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 168 GLU Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 236 VAL Chi-restraints excluded: chain P residue 376 GLN Chi-restraints excluded: chain P residue 439 VAL Chi-restraints excluded: chain P residue 455 LEU Chi-restraints excluded: chain P residue 473 VAL Chi-restraints excluded: chain b residue 46 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain c residue 88 ASP Chi-restraints excluded: chain c residue 127 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 152 ILE Chi-restraints excluded: chain c residue 170 GLU Chi-restraints excluded: chain c residue 177 ILE Chi-restraints excluded: chain c residue 195 THR Chi-restraints excluded: chain c residue 210 GLU Chi-restraints excluded: chain g residue 89 GLN Chi-restraints excluded: chain g residue 100 LEU Chi-restraints excluded: chain g residue 109 GLN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 285 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 449 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 65 GLN ** U 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112233 restraints weight = 59726.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111740 restraints weight = 52995.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112506 restraints weight = 52087.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113130 restraints weight = 38980.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113194 restraints weight = 33147.988| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 36854 Z= 0.203 Angle : 0.632 16.424 49840 Z= 0.324 Chirality : 0.047 0.248 5616 Planarity : 0.004 0.061 6505 Dihedral : 5.414 75.574 5092 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.26 % Allowed : 21.88 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -2.10 (0.12), residues: 4623 helix: -0.77 (0.12), residues: 1956 sheet: -1.62 (0.21), residues: 610 loop : -1.86 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 353 TYR 0.021 0.002 TYR P 423 PHE 0.019 0.002 PHE M 196 TRP 0.038 0.002 TRP M 433 HIS 0.007 0.001 HIS U 97 Details of bonding type rmsd covalent geometry : bond 0.00488 (36854) covalent geometry : angle 0.63172 (49840) hydrogen bonds : bond 0.03709 ( 1199) hydrogen bonds : angle 4.89398 ( 3435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6224.95 seconds wall clock time: 108 minutes 8.63 seconds (6488.63 seconds total)