Starting phenix.real_space_refine on Mon Sep 30 07:10:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/09_2024/8uxw_42787_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/09_2024/8uxw_42787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/09_2024/8uxw_42787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/09_2024/8uxw_42787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/09_2024/8uxw_42787_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxw_42787/09_2024/8uxw_42787_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 21 5.49 5 Mg 10 5.21 5 S 230 5.16 5 C 24684 2.51 5 N 6643 2.21 5 O 7441 1.98 5 H 38330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 287 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 77359 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 6226 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 379} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 6153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6153 Classifications: {'peptide': 387} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5576 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 5153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5153 Classifications: {'peptide': 316} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2781 Classifications: {'peptide': 168} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "G" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2362 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "H" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5758 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.95, per 1000 atoms: 0.35 Number of scatterers: 77359 At special positions: 0 Unit cell: (129.216, 205.938, 227.474, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 230 16.00 P 21 15.00 Mg 10 11.99 O 7441 8.00 N 6643 7.00 C 24684 6.00 H 38330 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 217 " - pdb=" SG CYS N 257 " distance=2.07 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: 14.15 Conformation dependent library (CDL) restraints added in 4.5 seconds 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9168 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 72 sheets defined 48.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.580A pdb=" N LYS A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 135 through 149 removed outlier: 3.565A pdb=" N ARG A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.542A pdb=" N ALA A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.556A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.679A pdb=" N TYR A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 341 through 366 removed outlier: 3.715A pdb=" N SER A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.585A pdb=" N GLU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.550A pdb=" N GLN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.029A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.653A pdb=" N GLN B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.665A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.141A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 325 Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.044A pdb=" N ARG B 332 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 361 removed outlier: 3.608A pdb=" N ASP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.817A pdb=" N TRP B 368 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 378 removed outlier: 3.731A pdb=" N GLU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.613A pdb=" N LYS B 384 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 296 Processing helix chain 'C' and resid 316 through 330 Processing helix chain 'D' and resid 8 through 21 removed outlier: 3.660A pdb=" N SER D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.604A pdb=" N ASN D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 120 through 140 Processing helix chain 'D' and resid 143 through 155 removed outlier: 3.992A pdb=" N SER D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 removed outlier: 3.848A pdb=" N VAL D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 removed outlier: 6.696A pdb=" N ALA D 208 " --> pdb=" O ARG D 205 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 209 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN D 210 " --> pdb=" O PRO D 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 210' Processing helix chain 'D' and resid 223 through 227 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.604A pdb=" N VAL D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 297 removed outlier: 3.872A pdb=" N LYS D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 42 through 55 removed outlier: 4.386A pdb=" N ARG E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 84 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 125 through 150 removed outlier: 3.749A pdb=" N SER E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 164 through 167 Processing helix chain 'E' and resid 168 through 172 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 36 through 41 removed outlier: 3.571A pdb=" N VAL F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 80 through 97 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 166 removed outlier: 5.007A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 168 No H-bonds generated for 'chain 'F' and resid 167 through 168' Processing helix chain 'G' and resid 2 through 6 removed outlier: 4.168A pdb=" N THR G 5 " --> pdb=" O THR G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.718A pdb=" N ILE G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 49 Proline residue: G 41 - end of helix removed outlier: 3.607A pdb=" N ILE G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 60 Processing helix chain 'G' and resid 69 through 87 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 100 through 116 Processing helix chain 'G' and resid 122 through 138 removed outlier: 3.691A pdb=" N LEU G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 148 Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 92 removed outlier: 3.892A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.865A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET H 123 " --> pdb=" O MET H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 Processing helix chain 'H' and resid 172 through 175 removed outlier: 3.586A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 204 through 217 Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 234 through 237 Processing helix chain 'H' and resid 252 through 263 Proline residue: H 258 - end of helix removed outlier: 4.590A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 291 removed outlier: 3.546A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.425A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.693A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 Processing helix chain 'I' and resid 55 through 62 Processing helix chain 'I' and resid 78 through 92 removed outlier: 4.047A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 112 through 126 removed outlier: 4.003A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET I 123 " --> pdb=" O MET I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 143 removed outlier: 4.046A pdb=" N TYR I 143 " --> pdb=" O VAL I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.713A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 202 through 217 removed outlier: 3.789A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 252 through 260 Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 261 through 262 No H-bonds generated for 'chain 'I' and resid 261 through 262' Processing helix chain 'I' and resid 263 through 268 Processing helix chain 'I' and resid 273 through 285 Processing helix chain 'I' and resid 288 through 295 removed outlier: 4.260A pdb=" N ASP I 292 " --> pdb=" O ILE I 289 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR I 294 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 removed outlier: 4.142A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 337 through 347 Processing helix chain 'I' and resid 351 through 355 removed outlier: 4.354A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 removed outlier: 5.688A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 373 removed outlier: 4.341A pdb=" N HIS I 371 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS I 373 " --> pdb=" O VAL I 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 61 Processing helix chain 'M' and resid 78 through 92 Processing helix chain 'M' and resid 97 through 101 Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.774A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 Processing helix chain 'M' and resid 181 through 193 Processing helix chain 'M' and resid 194 through 197 Processing helix chain 'M' and resid 202 through 214 Processing helix chain 'M' and resid 222 through 231 Processing helix chain 'M' and resid 252 through 260 Proline residue: M 258 - end of helix Processing helix chain 'M' and resid 261 through 262 No H-bonds generated for 'chain 'M' and resid 261 through 262' Processing helix chain 'M' and resid 263 through 268 Processing helix chain 'M' and resid 273 through 285 Processing helix chain 'M' and resid 289 through 295 Processing helix chain 'M' and resid 301 through 306 removed outlier: 4.357A pdb=" N TYR M 306 " --> pdb=" O THR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 321 Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 337 through 349 Processing helix chain 'M' and resid 350 through 355 removed outlier: 3.592A pdb=" N GLN M 353 " --> pdb=" O SER M 350 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 removed outlier: 5.690A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 374 removed outlier: 3.735A pdb=" N ARG M 372 " --> pdb=" O SER M 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 78 through 92 Processing helix chain 'N' and resid 97 through 101 Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.949A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 145 removed outlier: 3.649A pdb=" N SER N 141 " --> pdb=" O GLN N 137 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 194 removed outlier: 3.568A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 197 No H-bonds generated for 'chain 'N' and resid 195 through 197' Processing helix chain 'N' and resid 202 through 217 removed outlier: 4.213A pdb=" N LYS N 215 " --> pdb=" O ASP N 211 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS N 217 " --> pdb=" O LYS N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 232 removed outlier: 3.547A pdb=" N ALA N 231 " --> pdb=" O MET N 227 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER N 232 " --> pdb=" O ALA N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 260 Proline residue: N 258 - end of helix Processing helix chain 'N' and resid 261 through 262 No H-bonds generated for 'chain 'N' and resid 261 through 262' Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 273 through 285 Processing helix chain 'N' and resid 289 through 295 Processing helix chain 'N' and resid 301 through 305 Processing helix chain 'N' and resid 308 through 321 Processing helix chain 'N' and resid 337 through 347 Processing helix chain 'N' and resid 359 through 366 removed outlier: 3.677A pdb=" N GLU N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 374 removed outlier: 4.084A pdb=" N ARG N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 Processing helix chain 'O' and resid 78 through 92 Processing helix chain 'O' and resid 97 through 101 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.964A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 145 removed outlier: 3.581A pdb=" N TYR O 143 " --> pdb=" O VAL O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 197 removed outlier: 4.204A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 217 removed outlier: 3.553A pdb=" N ILE O 208 " --> pdb=" O ALA O 204 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS O 215 " --> pdb=" O ASP O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 232 Processing helix chain 'O' and resid 252 through 260 Proline residue: O 258 - end of helix Processing helix chain 'O' and resid 261 through 262 No H-bonds generated for 'chain 'O' and resid 261 through 262' Processing helix chain 'O' and resid 263 through 268 Processing helix chain 'O' and resid 273 through 285 Processing helix chain 'O' and resid 289 through 295 Processing helix chain 'O' and resid 301 through 305 Processing helix chain 'O' and resid 308 through 321 Processing helix chain 'O' and resid 337 through 347 Processing helix chain 'O' and resid 351 through 355 Processing helix chain 'O' and resid 359 through 366 Processing helix chain 'O' and resid 367 through 373 Processing helix chain 'P' and resid 55 through 61 Processing helix chain 'P' and resid 78 through 92 Processing helix chain 'P' and resid 97 through 101 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.890A pdb=" N ARG P 116 " --> pdb=" O PRO P 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET P 123 " --> pdb=" O MET P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 146 Processing helix chain 'P' and resid 181 through 194 removed outlier: 3.563A pdb=" N THR P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 197 No H-bonds generated for 'chain 'P' and resid 195 through 197' Processing helix chain 'P' and resid 202 through 217 removed outlier: 3.581A pdb=" N GLU P 207 " --> pdb=" O THR P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 232 Processing helix chain 'P' and resid 252 through 260 Proline residue: P 258 - end of helix Processing helix chain 'P' and resid 261 through 262 No H-bonds generated for 'chain 'P' and resid 261 through 262' Processing helix chain 'P' and resid 263 through 268 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 289 through 295 Processing helix chain 'P' and resid 301 through 305 Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 334 through 336 No H-bonds generated for 'chain 'P' and resid 334 through 336' Processing helix chain 'P' and resid 337 through 349 Processing helix chain 'P' and resid 351 through 355 removed outlier: 4.371A pdb=" N GLN P 354 " --> pdb=" O THR P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 366 removed outlier: 3.794A pdb=" N GLU P 364 " --> pdb=" O GLN P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 369 through 374 Processing helix chain 'Q' and resid 55 through 61 Processing helix chain 'Q' and resid 78 through 92 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.918A pdb=" N ARG Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 146 Processing helix chain 'Q' and resid 181 through 195 removed outlier: 4.020A pdb=" N GLU Q 195 " --> pdb=" O LYS Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 217 removed outlier: 3.753A pdb=" N GLU Q 207 " --> pdb=" O THR Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 233 Processing helix chain 'Q' and resid 234 through 237 Processing helix chain 'Q' and resid 252 through 257 removed outlier: 3.510A pdb=" N CYS Q 257 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 262 Processing helix chain 'Q' and resid 263 through 268 Processing helix chain 'Q' and resid 273 through 285 Processing helix chain 'Q' and resid 286 through 294 removed outlier: 3.655A pdb=" N ARG Q 290 " --> pdb=" O ASP Q 286 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 305 Processing helix chain 'Q' and resid 308 through 321 Processing helix chain 'Q' and resid 334 through 336 No H-bonds generated for 'chain 'Q' and resid 334 through 336' Processing helix chain 'Q' and resid 337 through 349 Processing helix chain 'Q' and resid 350 through 353 Processing helix chain 'Q' and resid 359 through 363 Processing helix chain 'Q' and resid 366 through 368 No H-bonds generated for 'chain 'Q' and resid 366 through 368' Processing helix chain 'Q' and resid 369 through 374 Processing helix chain 'R' and resid 55 through 61 Processing helix chain 'R' and resid 78 through 92 Processing helix chain 'R' and resid 97 through 101 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.919A pdb=" N ARG R 116 " --> pdb=" O PRO R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.729A pdb=" N SER R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 194 Processing helix chain 'R' and resid 195 through 197 No H-bonds generated for 'chain 'R' and resid 195 through 197' Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.957A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE R 208 " --> pdb=" O ALA R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 230 Processing helix chain 'R' and resid 231 through 236 removed outlier: 6.877A pdb=" N SER R 234 " --> pdb=" O ALA R 231 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER R 235 " --> pdb=" O SER R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 260 Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 261 through 262 No H-bonds generated for 'chain 'R' and resid 261 through 262' Processing helix chain 'R' and resid 263 through 268 Processing helix chain 'R' and resid 273 through 285 removed outlier: 3.582A pdb=" N CYS R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 295 Processing helix chain 'R' and resid 301 through 306 removed outlier: 4.342A pdb=" N TYR R 306 " --> pdb=" O THR R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'R' and resid 337 through 349 Processing helix chain 'R' and resid 351 through 355 removed outlier: 4.280A pdb=" N GLN R 354 " --> pdb=" O THR R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 364 Processing helix chain 'R' and resid 366 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.459A pdb=" N ILE A 8 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR A 129 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N MET A 10 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 126 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA A 158 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 128 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.583A pdb=" N ILE A 330 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 271 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 30 removed outlier: 6.754A pdb=" N ILE B 6 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR B 106 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU B 8 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 9 removed outlier: 6.803A pdb=" N VAL C 372 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 362 " --> pdb=" O TYR C 353 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 349 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 16 through 19 removed outlier: 4.546A pdb=" N GLU C 16 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 35 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU C 37 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.602A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 79 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 103 through 108 removed outlier: 3.741A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.877A pdb=" N LYS C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER C 174 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 198 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 208 through 213 removed outlier: 3.804A pdb=" N SER C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 243 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 254 through 261 removed outlier: 6.588A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN C 278 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS C 286 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN C 280 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 162 removed outlier: 6.991A pdb=" N GLU D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AC6, first strand: chain 'F' and resid 47 through 56 removed outlier: 5.435A pdb=" N LYS F 49 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N SER F 65 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.629A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'I' and resid 29 through 32 removed outlier: 4.113A pdb=" N THR I 106 " --> pdb=" O CYS I 10 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'M' and resid 29 through 32 removed outlier: 4.732A pdb=" N ASN M 12 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'M' and resid 176 through 178 removed outlier: 6.340A pdb=" N ASN M 297 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 176 through 178 removed outlier: 3.612A pdb=" N GLN O 41 " --> pdb=" O ALA M 170 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.759A pdb=" N THR N 106 " --> pdb=" O CYS N 10 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN N 12 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'N' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'N' and resid 169 through 170 removed outlier: 6.395A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU N 153 " --> pdb=" O SER N 300 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN N 297 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 238 through 241 Processing sheet with id=AF4, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.624A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 53 through 54 Processing sheet with id=AF6, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AF7, first strand: chain 'O' and resid 169 through 170 Processing sheet with id=AF8, first strand: chain 'O' and resid 169 through 170 removed outlier: 6.521A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN O 297 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 238 through 241 Processing sheet with id=AG1, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.734A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N CYS P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 53 through 54 Processing sheet with id=AG3, first strand: chain 'P' and resid 71 through 72 Processing sheet with id=AG4, first strand: chain 'P' and resid 169 through 170 Processing sheet with id=AG5, first strand: chain 'P' and resid 169 through 170 removed outlier: 6.445A pdb=" N ASN P 297 " --> pdb=" O ILE P 330 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 238 through 241 Processing sheet with id=AG7, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.767A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR Q 106 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N CYS Q 10 " --> pdb=" O THR Q 106 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AG9, first strand: chain 'Q' and resid 71 through 72 Processing sheet with id=AH1, first strand: chain 'Q' and resid 169 through 170 Processing sheet with id=AH2, first strand: chain 'Q' and resid 169 through 170 removed outlier: 6.470A pdb=" N ASN Q 297 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id=AH4, first strand: chain 'R' and resid 29 through 32 removed outlier: 6.523A pdb=" N LEU R 8 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR R 106 " --> pdb=" O LEU R 8 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N CYS R 10 " --> pdb=" O THR R 106 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 53 through 54 Processing sheet with id=AH6, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AH7, first strand: chain 'R' and resid 169 through 170 Processing sheet with id=AH8, first strand: chain 'R' and resid 169 through 170 Processing sheet with id=AH9, first strand: chain 'R' and resid 238 through 241 1933 hydrogen bonds defined for protein. 5043 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: 32.18 Time building geometry restraints manager: 17.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 0.98: 846 0.98 - 1.19: 37421 1.19 - 1.40: 14272 1.40 - 1.61: 25290 1.61 - 1.82: 396 Bond restraints: 78225 Sorted by residual: bond pdb=" NH2 ARG I 210 " pdb="HH21 ARG I 210 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR P 278 " pdb=" H THR P 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG D 162 " pdb="HH22 ARG D 162 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 TYR B 143 " pdb=" HE1 TYR B 143 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLU Q 107 " pdb=" H GLU Q 107 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 78220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 134924 4.61 - 9.22: 6257 9.22 - 13.84: 93 13.84 - 18.45: 4 18.45 - 23.06: 8 Bond angle restraints: 141286 Sorted by residual: angle pdb=" PA ATP B 902 " pdb=" O3A ATP B 902 " pdb=" PB ATP B 902 " ideal model delta sigma weight residual 136.83 121.93 14.90 1.00e+00 1.00e+00 2.22e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 125.32 14.55 1.00e+00 1.00e+00 2.12e+02 angle pdb=" O2B ADP M 802 " pdb=" PB ADP M 802 " pdb=" O3B ADP M 802 " ideal model delta sigma weight residual 119.90 96.84 23.06 3.00e+00 1.11e-01 5.91e+01 angle pdb=" O1B ADP I 802 " pdb=" PB ADP I 802 " pdb=" O2B ADP I 802 " ideal model delta sigma weight residual 119.90 96.90 23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" O1B ADP P 802 " pdb=" PB ADP P 802 " pdb=" O3B ADP P 802 " ideal model delta sigma weight residual 119.90 97.12 22.78 3.00e+00 1.11e-01 5.77e+01 ... (remaining 141281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 35098 31.11 - 62.22: 1573 62.22 - 93.33: 253 93.33 - 124.44: 8 124.44 - 155.54: 8 Dihedral angle restraints: 36940 sinusoidal: 20227 harmonic: 16713 Sorted by residual: dihedral pdb=" O1B ADP M 802 " pdb=" O3A ADP M 802 " pdb=" PB ADP M 802 " pdb=" PA ADP M 802 " ideal model delta sinusoidal sigma weight residual -60.00 95.54 -155.54 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP Q 802 " pdb=" O3A ADP Q 802 " pdb=" PA ADP Q 802 " pdb=" PB ADP Q 802 " ideal model delta sinusoidal sigma weight residual -60.00 93.12 -153.12 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" O1B ADP R 802 " pdb=" O3A ADP R 802 " pdb=" PB ADP R 802 " pdb=" PA ADP R 802 " ideal model delta sinusoidal sigma weight residual -60.00 92.18 -152.19 1 2.00e+01 2.50e-03 4.52e+01 ... (remaining 36937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4674 0.123 - 0.245: 1174 0.245 - 0.368: 130 0.368 - 0.491: 10 0.491 - 0.613: 2 Chirality restraints: 5990 Sorted by residual: chirality pdb=" CA ARG D 287 " pdb=" N ARG D 287 " pdb=" C ARG D 287 " pdb=" CB ARG D 287 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" CA ARG Q 95 " pdb=" N ARG Q 95 " pdb=" C ARG Q 95 " pdb=" CB ARG Q 95 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA CYS F 167 " pdb=" N CYS F 167 " pdb=" C CYS F 167 " pdb=" CB CYS F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 5987 not shown) Planarity restraints: 11609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP O 340 " 0.324 2.00e-02 2.50e+03 1.21e-01 5.89e+02 pdb=" CG TRP O 340 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP O 340 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP O 340 " -0.124 2.00e-02 2.50e+03 pdb=" NE1 TRP O 340 " -0.135 2.00e-02 2.50e+03 pdb=" CE2 TRP O 340 " -0.098 2.00e-02 2.50e+03 pdb=" CE3 TRP O 340 " -0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 340 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 340 " -0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP O 340 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP O 340 " 0.087 2.00e-02 2.50e+03 pdb=" HE1 TRP O 340 " -0.059 2.00e-02 2.50e+03 pdb=" HE3 TRP O 340 " -0.126 2.00e-02 2.50e+03 pdb=" HZ2 TRP O 340 " 0.110 2.00e-02 2.50e+03 pdb=" HZ3 TRP O 340 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP O 340 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 340 " 0.335 2.00e-02 2.50e+03 1.21e-01 5.81e+02 pdb=" CG TRP M 340 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP M 340 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP M 340 " -0.105 2.00e-02 2.50e+03 pdb=" NE1 TRP M 340 " -0.137 2.00e-02 2.50e+03 pdb=" CE2 TRP M 340 " -0.081 2.00e-02 2.50e+03 pdb=" CE3 TRP M 340 " -0.113 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 340 " 0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 340 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP M 340 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 TRP M 340 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TRP M 340 " -0.062 2.00e-02 2.50e+03 pdb=" HE3 TRP M 340 " -0.139 2.00e-02 2.50e+03 pdb=" HZ2 TRP M 340 " 0.118 2.00e-02 2.50e+03 pdb=" HZ3 TRP M 340 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP M 340 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 387 " 0.309 2.00e-02 2.50e+03 1.18e-01 5.60e+02 pdb=" CG TRP A 387 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 387 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 387 " -0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP A 387 " -0.130 2.00e-02 2.50e+03 pdb=" CE2 TRP A 387 " -0.044 2.00e-02 2.50e+03 pdb=" CE3 TRP A 387 " -0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 387 " 0.052 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 387 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 387 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP A 387 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TRP A 387 " -0.144 2.00e-02 2.50e+03 pdb=" HE3 TRP A 387 " -0.165 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 387 " 0.119 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 387 " -0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP A 387 " 0.140 2.00e-02 2.50e+03 ... (remaining 11606 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 4779 2.17 - 2.78: 134319 2.78 - 3.38: 231288 3.38 - 3.99: 314703 3.99 - 4.60: 457706 Nonbonded interactions: 1142795 Sorted by model distance: nonbonded pdb=" HG SER B 275 " pdb=" OE1 GLU B 316 " model vdw 1.560 2.450 nonbonded pdb=" OD1 ASP C 328 " pdb=" HG1 THR O 351 " model vdw 1.584 2.450 nonbonded pdb=" HG SER B 311 " pdb=" OE1 GLU F 31 " model vdw 1.587 2.450 nonbonded pdb=" OE2 GLU A 106 " pdb=" HG SER A 149 " model vdw 1.590 2.450 nonbonded pdb=" OE1 GLU O 270 " pdb=" HG1 THR P 202 " model vdw 1.595 2.450 ... (remaining 1142790 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 'H' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'I' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'M' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = chain 'N' selection = (chain 'O' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'P' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'Q' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'R' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 65.280 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: 0.980 Extract box with map and model: 2.480 Check model and map are aligned: 0.450 Set scattering table: 0.540 Process input model: 129.260 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.250 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:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.013 0.141 39895 Z= 0.844 Angle : 1.916 23.059 54139 Z= 1.259 Chirality : 0.104 0.613 5990 Planarity : 0.017 0.387 6962 Dihedral : 15.354 155.545 14846 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 2.69 % Allowed : 5.81 % Favored : 91.50 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.11), residues: 4854 helix: -1.74 (0.10), residues: 1937 sheet: -0.26 (0.19), residues: 627 loop : 0.18 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.222 0.031 TRP M 340 HIS 0.016 0.004 HIS Q 371 PHE 0.117 0.013 PHE F 101 TYR 0.176 0.018 TYR B 127 ARG 0.017 0.002 ARG F 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 1217 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1104 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.6906 (mtt-85) cc_final: 0.6021 (mtm180) REVERT: A 226 ASP cc_start: 0.7315 (m-30) cc_final: 0.6885 (m-30) REVERT: A 228 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6766 (m-40) REVERT: A 235 LYS cc_start: 0.6483 (pttp) cc_final: 0.6270 (ptmt) REVERT: A 239 ARG cc_start: 0.6322 (mtt180) cc_final: 0.5822 (mtm-85) REVERT: A 253 LYS cc_start: 0.6842 (mppt) cc_final: 0.6306 (mptt) REVERT: A 297 GLU cc_start: 0.6379 (mt-10) cc_final: 0.5385 (mp0) REVERT: A 340 LYS cc_start: 0.7326 (tptp) cc_final: 0.6684 (tttt) REVERT: A 406 LYS cc_start: 0.7013 (pttp) cc_final: 0.6740 (ptpp) REVERT: B 6 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 21 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7882 (mtmm) REVERT: B 68 LYS cc_start: 0.6426 (mtmt) cc_final: 0.6012 (mtmt) REVERT: B 72 GLU cc_start: 0.7770 (tt0) cc_final: 0.7441 (tt0) REVERT: B 73 ASN cc_start: 0.7177 (m-40) cc_final: 0.6589 (t0) REVERT: B 96 ILE cc_start: 0.7657 (mm) cc_final: 0.7184 (pt) REVERT: B 118 LYS cc_start: 0.6512 (ttpt) cc_final: 0.6250 (mtmm) REVERT: B 187 ARG cc_start: 0.6975 (mtt180) cc_final: 0.6758 (mtt90) REVERT: B 211 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6305 (mt-10) REVERT: B 224 GLU cc_start: 0.6699 (pt0) cc_final: 0.6488 (mt-10) REVERT: B 228 LYS cc_start: 0.6537 (ttpt) cc_final: 0.5940 (ttpp) REVERT: B 295 ARG cc_start: 0.6773 (mtp-110) cc_final: 0.6117 (mtt180) REVERT: C 22 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7126 (mp10) REVERT: C 73 CYS cc_start: 0.6303 (m) cc_final: 0.5780 (p) REVERT: C 83 GLU cc_start: 0.7140 (tt0) cc_final: 0.6262 (tp30) REVERT: C 91 LYS cc_start: 0.7445 (ttpt) cc_final: 0.6542 (tptm) REVERT: C 250 SER cc_start: 0.8246 (p) cc_final: 0.7953 (m) REVERT: C 251 GLN cc_start: 0.7848 (mt0) cc_final: 0.6647 (pp30) REVERT: C 252 LEU cc_start: 0.6943 (mm) cc_final: 0.6424 (mt) REVERT: C 327 MET cc_start: 0.7641 (mtp) cc_final: 0.7399 (mtp) REVERT: C 359 ASN cc_start: 0.6661 (m110) cc_final: 0.6178 (t0) REVERT: D 3 SER cc_start: 0.8362 (t) cc_final: 0.8156 (p) REVERT: D 23 ASN cc_start: 0.7655 (t0) cc_final: 0.7400 (t0) REVERT: D 28 ASP cc_start: 0.8003 (t0) cc_final: 0.7706 (t70) REVERT: D 47 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7238 (mttp) REVERT: D 56 MET cc_start: 0.8321 (ttm) cc_final: 0.8012 (ttm) REVERT: D 73 GLN cc_start: 0.7361 (tt0) cc_final: 0.7051 (mt0) REVERT: D 113 MET cc_start: 0.7281 (tpp) cc_final: 0.6767 (mmt) REVERT: D 143 ASN cc_start: 0.7243 (t0) cc_final: 0.7011 (t0) REVERT: D 157 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6795 (mtm) REVERT: D 172 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6420 (mt-10) REVERT: D 255 ARG cc_start: 0.5740 (mtm110) cc_final: 0.5483 (mtt90) REVERT: D 283 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7230 (mmt180) REVERT: D 284 MET cc_start: 0.7757 (mtt) cc_final: 0.7529 (mtt) REVERT: E 88 ASN cc_start: 0.5608 (t0) cc_final: 0.5395 (t0) REVERT: E 94 ARG cc_start: 0.7601 (mtp180) cc_final: 0.6996 (mtp180) REVERT: E 98 SER cc_start: 0.7067 (t) cc_final: 0.6655 (m) REVERT: F 31 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: F 57 GLU cc_start: 0.7241 (tp30) cc_final: 0.6876 (mp0) REVERT: F 58 GLN cc_start: 0.7552 (mp-120) cc_final: 0.6096 (tp-100) REVERT: F 81 GLU cc_start: 0.6930 (mp0) cc_final: 0.6126 (mm-30) REVERT: F 88 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6223 (ttm110) REVERT: F 97 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6893 (mmm160) REVERT: F 107 LYS cc_start: 0.7154 (mmmm) cc_final: 0.6900 (mptm) REVERT: F 148 GLU cc_start: 0.6881 (tt0) cc_final: 0.6680 (tt0) REVERT: G 18 GLU cc_start: 0.7433 (pt0) cc_final: 0.6381 (mm-30) REVERT: G 20 ASP cc_start: 0.7673 (m-30) cc_final: 0.7259 (t0) REVERT: G 71 GLU cc_start: 0.6050 (mp0) cc_final: 0.5649 (pm20) REVERT: G 82 ASP cc_start: 0.6164 (m-30) cc_final: 0.5824 (m-30) REVERT: G 102 GLU cc_start: 0.7015 (tt0) cc_final: 0.6373 (mp0) REVERT: G 132 LYS cc_start: 0.7202 (mttm) cc_final: 0.6871 (mtmm) REVERT: G 135 GLU cc_start: 0.7082 (tt0) cc_final: 0.6706 (tt0) REVERT: H 72 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: H 83 GLU cc_start: 0.6827 (pt0) cc_final: 0.6583 (tm-30) REVERT: H 121 GLN cc_start: 0.6607 (tt0) cc_final: 0.6276 (tm-30) REVERT: H 141 SER cc_start: 0.7935 (t) cc_final: 0.7706 (m) REVERT: H 165 ILE cc_start: 0.7578 (tt) cc_final: 0.7359 (mt) REVERT: H 191 LYS cc_start: 0.6548 (tttp) cc_final: 0.6092 (ttmt) REVERT: H 206 ARG cc_start: 0.6742 (ttm-80) cc_final: 0.5637 (ttm110) REVERT: H 225 ASN cc_start: 0.7570 (m-40) cc_final: 0.6875 (t0) REVERT: H 234 SER cc_start: 0.6728 (m) cc_final: 0.6404 (t) REVERT: H 269 MET cc_start: 0.8362 (ttm) cc_final: 0.8103 (ttp) REVERT: H 313 MET cc_start: 0.7697 (tpt) cc_final: 0.7474 (tpt) REVERT: H 328 LYS cc_start: 0.6863 (mmmm) cc_final: 0.6546 (mppt) REVERT: I 11 ASP cc_start: 0.6266 (t0) cc_final: 0.6038 (t0) REVERT: I 25 ASP cc_start: 0.6784 (m-30) cc_final: 0.6560 (p0) REVERT: I 50 LYS cc_start: 0.7482 (mmpt) cc_final: 0.7021 (mtpm) REVERT: I 68 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7237 (mttt) REVERT: I 92 ASN cc_start: 0.7425 (m-40) cc_final: 0.7170 (m-40) REVERT: I 122 ILE cc_start: 0.7580 (pt) cc_final: 0.7204 (mm) REVERT: I 169 TYR cc_start: 0.6596 (m-80) cc_final: 0.5396 (t80) REVERT: I 215 LYS cc_start: 0.7700 (mtpp) cc_final: 0.7293 (mttp) REVERT: I 296 ASN cc_start: 0.7243 (t0) cc_final: 0.6879 (t0) REVERT: I 305 MET cc_start: 0.8155 (mmm) cc_final: 0.7826 (mmm) REVERT: I 336 LYS cc_start: 0.6832 (ptpp) cc_final: 0.6530 (ttpt) REVERT: I 362 TYR cc_start: 0.6950 (t80) cc_final: 0.6669 (t80) REVERT: M 78 ASN cc_start: 0.7435 (t0) cc_final: 0.6952 (t0) REVERT: M 96 VAL cc_start: 0.7487 (m) cc_final: 0.7275 (m) REVERT: M 194 THR cc_start: 0.8079 (m) cc_final: 0.7633 (p) REVERT: M 202 THR cc_start: 0.7555 (m) cc_final: 0.7220 (p) REVERT: M 224 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7414 (pm20) REVERT: M 263 GLN cc_start: 0.7739 (mt0) cc_final: 0.7315 (mt0) REVERT: N 47 MET cc_start: 0.1361 (ttp) cc_final: 0.0488 (ttm) REVERT: N 225 ASN cc_start: 0.6778 (t0) cc_final: 0.6478 (m-40) REVERT: N 276 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6980 (mt-10) REVERT: N 328 LYS cc_start: 0.7428 (tptt) cc_final: 0.6951 (tppp) REVERT: N 355 MET cc_start: 0.8059 (mtt) cc_final: 0.7802 (mtp) REVERT: N 360 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7123 (tp-100) REVERT: O 41 GLN cc_start: 0.6989 (tp40) cc_final: 0.6730 (mm-40) REVERT: O 68 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7691 (ptpp) REVERT: O 100 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7609 (mt-10) REVERT: O 113 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7240 (mmtp) REVERT: O 118 LYS cc_start: 0.7282 (mttm) cc_final: 0.6682 (mtpm) REVERT: O 206 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.6586 (ttp-110) REVERT: O 276 GLU cc_start: 0.6904 (tt0) cc_final: 0.6431 (tt0) REVERT: O 284 LYS cc_start: 0.7966 (mttm) cc_final: 0.7534 (mtpm) REVERT: O 286 ASP cc_start: 0.6881 (t0) cc_final: 0.6518 (m-30) REVERT: O 326 LYS cc_start: 0.7368 (ptpp) cc_final: 0.6438 (mmmt) REVERT: O 328 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7084 (mttp) REVERT: O 359 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7672 (tptp) REVERT: P 82 MET cc_start: 0.7772 (tpt) cc_final: 0.6931 (tpt) REVERT: P 283 MET cc_start: 0.8200 (mmm) cc_final: 0.7974 (mmp) REVERT: P 326 LYS cc_start: 0.7660 (pttp) cc_final: 0.7454 (pttm) REVERT: P 359 LYS cc_start: 0.7195 (ptmm) cc_final: 0.6816 (tttt) REVERT: Q 6 THR cc_start: 0.8029 (p) cc_final: 0.7559 (t) REVERT: Q 34 ILE cc_start: 0.8353 (mt) cc_final: 0.7899 (pt) REVERT: Q 47 MET cc_start: 0.6248 (mmm) cc_final: 0.5405 (ptt) REVERT: Q 60 SER cc_start: 0.7986 (t) cc_final: 0.7690 (p) REVERT: Q 66 THR cc_start: 0.8303 (t) cc_final: 0.8056 (m) REVERT: Q 82 MET cc_start: 0.8272 (tpt) cc_final: 0.7748 (tpt) REVERT: Q 95 ARG cc_start: 0.6926 (ptp-170) cc_final: 0.6378 (ptp-110) REVERT: Q 167 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7331 (mm-30) REVERT: Q 190 MET cc_start: 0.7630 (mtm) cc_final: 0.7387 (mtp) REVERT: Q 215 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6949 (mmtp) REVERT: Q 224 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7795 (mp0) REVERT: Q 246 GLN cc_start: 0.7922 (mt0) cc_final: 0.7618 (mt0) REVERT: Q 291 LYS cc_start: 0.5649 (mttm) cc_final: 0.4643 (tmtm) REVERT: Q 314 GLN cc_start: 0.7972 (tt0) cc_final: 0.7624 (tt0) REVERT: Q 328 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6601 (ttpp) REVERT: Q 336 LYS cc_start: 0.7676 (tptm) cc_final: 0.7349 (tppp) REVERT: Q 354 GLN cc_start: 0.7645 (pm20) cc_final: 0.7059 (mm110) REVERT: R 25 ASP cc_start: 0.7944 (m-30) cc_final: 0.7599 (t70) REVERT: R 83 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7002 (mt-10) REVERT: R 100 GLU cc_start: 0.8143 (pt0) cc_final: 0.7825 (pt0) REVERT: R 167 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7248 (mm-30) REVERT: R 206 ARG cc_start: 0.6814 (tpp80) cc_final: 0.6356 (ttp-170) REVERT: R 215 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7301 (mptm) REVERT: R 234 SER cc_start: 0.5746 (OUTLIER) cc_final: 0.5418 (t) outliers start: 113 outliers final: 36 residues processed: 1162 average time/residue: 2.7822 time to fit residues: 3978.5586 Evaluate side-chains 725 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 681 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 234 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 383 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 313 ASN B 10 ASN B 48 GLN B 83 ASN B 173 HIS B 201 ASN B 335 ASN B 364 ASN C 209 HIS ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 292 GLN E 156 HIS F 10 ASN F 60 GLN F 120 ASN G 19 GLN G 106 ASN H 137 GLN I 41 GLN M 59 GLN N 137 GLN O 353 GLN O 360 GLN P 263 GLN Q 41 GLN Q 87 HIS Q 173 HIS R 49 GLN R 354 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39895 Z= 0.247 Angle : 0.737 9.141 54139 Z= 0.388 Chirality : 0.047 0.234 5990 Planarity : 0.006 0.088 6962 Dihedral : 11.045 145.131 5608 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.00 % Allowed : 13.77 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4854 helix: -0.70 (0.11), residues: 1945 sheet: -0.39 (0.17), residues: 876 loop : 0.64 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 356 HIS 0.006 0.001 HIS C 140 PHE 0.027 0.001 PHE B 277 TYR 0.024 0.001 TYR B 88 ARG 0.007 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 845 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 719 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7239 (pt0) cc_final: 0.6996 (pp20) REVERT: A 226 ASP cc_start: 0.6813 (m-30) cc_final: 0.6402 (m-30) REVERT: A 238 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.4952 (tt0) REVERT: A 239 ARG cc_start: 0.5999 (mtt180) cc_final: 0.5516 (mtm-85) REVERT: A 242 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5522 (mp0) REVERT: A 253 LYS cc_start: 0.6530 (mppt) cc_final: 0.6085 (mptt) REVERT: A 297 GLU cc_start: 0.6734 (mt-10) cc_final: 0.5774 (mp0) REVERT: A 302 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6290 (m-30) REVERT: A 340 LYS cc_start: 0.7397 (tptp) cc_final: 0.6793 (tttt) REVERT: A 356 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6862 (tm-30) REVERT: A 406 LYS cc_start: 0.6798 (pttp) cc_final: 0.6405 (ptpt) REVERT: B 6 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7216 (mt) REVERT: B 68 LYS cc_start: 0.6506 (mtmt) cc_final: 0.6091 (mtmt) REVERT: B 73 ASN cc_start: 0.7270 (m-40) cc_final: 0.6805 (t0) REVERT: B 96 ILE cc_start: 0.7671 (mm) cc_final: 0.7136 (pt) REVERT: B 118 LYS cc_start: 0.6217 (ttpt) cc_final: 0.5946 (mtmt) REVERT: B 152 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7786 (p) REVERT: B 228 LYS cc_start: 0.6474 (ttpt) cc_final: 0.5794 (ttpp) REVERT: B 244 ASP cc_start: 0.6992 (m-30) cc_final: 0.6743 (m-30) REVERT: B 295 ARG cc_start: 0.6663 (mtp180) cc_final: 0.5691 (mpt-90) REVERT: B 364 ASN cc_start: 0.7167 (m-40) cc_final: 0.6753 (t0) REVERT: C 22 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7165 (mp10) REVERT: C 83 GLU cc_start: 0.7053 (tt0) cc_final: 0.6101 (mp0) REVERT: C 91 LYS cc_start: 0.7364 (ttpt) cc_final: 0.6105 (tttt) REVERT: C 250 SER cc_start: 0.8269 (p) cc_final: 0.7989 (m) REVERT: C 251 GLN cc_start: 0.7601 (mt0) cc_final: 0.6117 (pp30) REVERT: C 252 LEU cc_start: 0.6793 (mm) cc_final: 0.6033 (mt) REVERT: C 327 MET cc_start: 0.7470 (mtp) cc_final: 0.7182 (mtp) REVERT: C 359 ASN cc_start: 0.6593 (m110) cc_final: 0.5879 (t0) REVERT: D 3 SER cc_start: 0.8054 (t) cc_final: 0.7854 (p) REVERT: D 13 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6173 (mt-10) REVERT: D 28 ASP cc_start: 0.8212 (t0) cc_final: 0.8008 (t70) REVERT: D 47 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7224 (mttp) REVERT: D 73 GLN cc_start: 0.7206 (tt0) cc_final: 0.6937 (mt0) REVERT: D 157 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6858 (mtm) REVERT: D 172 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6147 (mt-10) REVERT: D 185 ARG cc_start: 0.7767 (ptp-170) cc_final: 0.7410 (ptp-170) REVERT: D 255 ARG cc_start: 0.5719 (mtm110) cc_final: 0.5330 (mtt90) REVERT: E 58 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7061 (ptm160) REVERT: E 61 GLU cc_start: 0.7188 (tt0) cc_final: 0.6598 (pt0) REVERT: E 94 ARG cc_start: 0.7495 (mtp180) cc_final: 0.7028 (mtp180) REVERT: E 98 SER cc_start: 0.6781 (t) cc_final: 0.6476 (m) REVERT: F 58 GLN cc_start: 0.7407 (mp-120) cc_final: 0.6020 (tp-100) REVERT: F 81 GLU cc_start: 0.6774 (mp0) cc_final: 0.5896 (mm-30) REVERT: F 83 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6902 (mt-10) REVERT: F 97 ARG cc_start: 0.7239 (mmm160) cc_final: 0.6864 (mmm160) REVERT: F 107 LYS cc_start: 0.7034 (mmmm) cc_final: 0.6735 (mttt) REVERT: F 148 GLU cc_start: 0.6710 (tt0) cc_final: 0.6440 (tt0) REVERT: G 20 ASP cc_start: 0.7893 (m-30) cc_final: 0.7625 (t0) REVERT: G 54 GLN cc_start: 0.6563 (mm-40) cc_final: 0.5767 (tm-30) REVERT: G 102 GLU cc_start: 0.6800 (tt0) cc_final: 0.6102 (mp0) REVERT: G 135 GLU cc_start: 0.6558 (tt0) cc_final: 0.6295 (tt0) REVERT: H 45 VAL cc_start: 0.7628 (m) cc_final: 0.7371 (t) REVERT: H 72 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: H 123 MET cc_start: 0.7923 (tpp) cc_final: 0.6993 (mmt) REVERT: H 141 SER cc_start: 0.7781 (t) cc_final: 0.7471 (m) REVERT: H 191 LYS cc_start: 0.6424 (tttp) cc_final: 0.6211 (ttmt) REVERT: H 206 ARG cc_start: 0.6542 (ttm-80) cc_final: 0.5422 (ttm110) REVERT: H 225 ASN cc_start: 0.7494 (m-40) cc_final: 0.6946 (t0) REVERT: H 234 SER cc_start: 0.6909 (m) cc_final: 0.6549 (t) REVERT: H 269 MET cc_start: 0.8332 (ttm) cc_final: 0.8127 (ttm) REVERT: H 305 MET cc_start: 0.8618 (tpt) cc_final: 0.8242 (mmm) REVERT: H 328 LYS cc_start: 0.6894 (mmmm) cc_final: 0.6642 (mppt) REVERT: I 25 ASP cc_start: 0.6877 (m-30) cc_final: 0.6578 (p0) REVERT: I 50 LYS cc_start: 0.7338 (mmpt) cc_final: 0.6947 (mtpm) REVERT: I 68 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7297 (mttt) REVERT: I 95 ARG cc_start: 0.6545 (mtp85) cc_final: 0.6334 (mtt-85) REVERT: I 123 MET cc_start: 0.7098 (mmp) cc_final: 0.6660 (mmt) REVERT: I 169 TYR cc_start: 0.6608 (m-80) cc_final: 0.5406 (t80) REVERT: I 215 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7225 (mttp) REVERT: I 305 MET cc_start: 0.8206 (mmm) cc_final: 0.7900 (mmm) REVERT: I 336 LYS cc_start: 0.6964 (ptpp) cc_final: 0.6660 (ttpt) REVERT: M 83 GLU cc_start: 0.6850 (tt0) cc_final: 0.6437 (tm-30) REVERT: M 194 THR cc_start: 0.8104 (m) cc_final: 0.7659 (p) REVERT: M 202 THR cc_start: 0.7595 (m) cc_final: 0.7357 (p) REVERT: M 206 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7314 (ttm110) REVERT: M 224 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7255 (pm20) REVERT: M 227 MET cc_start: 0.8354 (mmt) cc_final: 0.7849 (mmt) REVERT: N 41 GLN cc_start: 0.7049 (pt0) cc_final: 0.6813 (pm20) REVERT: N 47 MET cc_start: 0.1219 (ttp) cc_final: 0.0559 (ttm) REVERT: N 225 ASN cc_start: 0.6958 (t0) cc_final: 0.6560 (m-40) REVERT: N 276 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6893 (mt-10) REVERT: N 299 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8308 (mtt) REVERT: N 328 LYS cc_start: 0.7525 (tptt) cc_final: 0.7100 (tptm) REVERT: N 360 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7161 (tp-100) REVERT: O 41 GLN cc_start: 0.6994 (tp40) cc_final: 0.6753 (mm-40) REVERT: O 68 LYS cc_start: 0.8003 (ptmt) cc_final: 0.7719 (ptpp) REVERT: O 100 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7456 (mt-10) REVERT: O 113 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7125 (mmtp) REVERT: O 118 LYS cc_start: 0.7129 (mttm) cc_final: 0.6640 (mtpm) REVERT: O 206 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.6394 (ttp-110) REVERT: O 227 MET cc_start: 0.7837 (tpt) cc_final: 0.7617 (mmm) REVERT: O 276 GLU cc_start: 0.6908 (tt0) cc_final: 0.6465 (tt0) REVERT: O 284 LYS cc_start: 0.7543 (mttm) cc_final: 0.7208 (mttm) REVERT: O 286 ASP cc_start: 0.6840 (t0) cc_final: 0.6559 (m-30) REVERT: O 326 LYS cc_start: 0.7220 (ptpp) cc_final: 0.6355 (mmmt) REVERT: O 328 LYS cc_start: 0.7710 (mtmt) cc_final: 0.6961 (tptm) REVERT: O 359 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7550 (tptp) REVERT: P 82 MET cc_start: 0.7717 (tpt) cc_final: 0.7033 (tpt) REVERT: P 141 SER cc_start: 0.7749 (t) cc_final: 0.7473 (m) REVERT: P 221 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8050 (tp) REVERT: P 355 MET cc_start: 0.8178 (mtm) cc_final: 0.7863 (mtt) REVERT: P 359 LYS cc_start: 0.7272 (ptmm) cc_final: 0.6838 (tttt) REVERT: Q 6 THR cc_start: 0.7939 (p) cc_final: 0.7477 (t) REVERT: Q 34 ILE cc_start: 0.8380 (mt) cc_final: 0.7977 (pt) REVERT: Q 47 MET cc_start: 0.6246 (mmm) cc_final: 0.5394 (ptt) REVERT: Q 60 SER cc_start: 0.7640 (t) cc_final: 0.7396 (p) REVERT: Q 167 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7218 (mm-30) REVERT: Q 190 MET cc_start: 0.7369 (mtm) cc_final: 0.6997 (mtp) REVERT: Q 246 GLN cc_start: 0.7941 (mt0) cc_final: 0.7569 (mt0) REVERT: Q 286 ASP cc_start: 0.6956 (t0) cc_final: 0.6501 (m-30) REVERT: Q 291 LYS cc_start: 0.5445 (mttm) cc_final: 0.4633 (tmtm) REVERT: Q 313 MET cc_start: 0.7992 (tpt) cc_final: 0.7581 (mmm) REVERT: Q 328 LYS cc_start: 0.7320 (ttmt) cc_final: 0.6605 (ttpp) REVERT: Q 336 LYS cc_start: 0.7611 (tptm) cc_final: 0.7266 (tppt) REVERT: Q 354 GLN cc_start: 0.7741 (pm20) cc_final: 0.7136 (mm110) REVERT: R 99 GLU cc_start: 0.7387 (pt0) cc_final: 0.6880 (pm20) REVERT: R 206 ARG cc_start: 0.6634 (tpp80) cc_final: 0.6095 (ttp-170) REVERT: R 215 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7326 (mptm) REVERT: R 225 ASN cc_start: 0.6435 (t0) cc_final: 0.6068 (m-40) REVERT: R 234 SER cc_start: 0.6070 (OUTLIER) cc_final: 0.5769 (t) outliers start: 126 outliers final: 49 residues processed: 794 average time/residue: 2.7582 time to fit residues: 2676.3514 Evaluate side-chains 687 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 626 time to evaluate : 7.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 51 ASP Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 234 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 369 optimal weight: 1.9990 chunk 302 optimal weight: 0.9990 chunk 122 optimal weight: 0.0670 chunk 444 optimal weight: 3.9990 chunk 480 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 441 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 356 optimal weight: 2.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 172 ASN D 254 ASN E 139 GLN F 120 ASN F 129 HIS G 19 GLN G 31 GLN H 162 ASN I 41 GLN ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 HIS M 88 HIS M 162 ASN M 173 HIS O 225 ASN P 173 HIS R 354 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39895 Z= 0.212 Angle : 0.626 7.786 54139 Z= 0.320 Chirality : 0.045 0.222 5990 Planarity : 0.004 0.067 6962 Dihedral : 9.904 152.950 5574 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.43 % Allowed : 14.89 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4854 helix: -0.11 (0.12), residues: 1944 sheet: -0.48 (0.17), residues: 875 loop : 0.74 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 356 HIS 0.005 0.001 HIS A 404 PHE 0.018 0.001 PHE B 277 TYR 0.018 0.001 TYR B 88 ARG 0.006 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 753 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 651 time to evaluate : 4.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7312 (pt0) cc_final: 0.7034 (pp20) REVERT: A 137 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5841 (mp0) REVERT: A 207 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6601 (tppt) REVERT: A 226 ASP cc_start: 0.6701 (m-30) cc_final: 0.6366 (m-30) REVERT: A 239 ARG cc_start: 0.6058 (mtt180) cc_final: 0.5537 (mtm-85) REVERT: A 242 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5824 (mp0) REVERT: A 253 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.6086 (mptt) REVERT: A 297 GLU cc_start: 0.6871 (mt-10) cc_final: 0.5810 (mp0) REVERT: A 302 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6244 (m-30) REVERT: A 340 LYS cc_start: 0.7300 (tptp) cc_final: 0.6852 (ttpt) REVERT: A 356 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6753 (tm-30) REVERT: A 406 LYS cc_start: 0.6827 (pttp) cc_final: 0.6399 (ptpt) REVERT: B 6 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7375 (mt) REVERT: B 10 ASN cc_start: 0.7052 (p0) cc_final: 0.6845 (p0) REVERT: B 68 LYS cc_start: 0.6573 (mtmt) cc_final: 0.6092 (mtmt) REVERT: B 73 ASN cc_start: 0.7393 (m-40) cc_final: 0.6922 (t0) REVERT: B 96 ILE cc_start: 0.7706 (mm) cc_final: 0.7339 (pt) REVERT: B 152 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7806 (p) REVERT: B 228 LYS cc_start: 0.6469 (ttpt) cc_final: 0.5801 (ttpp) REVERT: B 295 ARG cc_start: 0.6614 (mtp180) cc_final: 0.5639 (mpt-90) REVERT: B 364 ASN cc_start: 0.7179 (m-40) cc_final: 0.6725 (t0) REVERT: B 376 GLU cc_start: 0.7045 (pt0) cc_final: 0.6767 (pp20) REVERT: B 380 ARG cc_start: 0.7158 (tpp-160) cc_final: 0.6870 (tpp-160) REVERT: C 22 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7244 (mp10) REVERT: C 83 GLU cc_start: 0.7002 (tt0) cc_final: 0.6174 (mp0) REVERT: C 91 LYS cc_start: 0.7395 (ttpt) cc_final: 0.5987 (tptp) REVERT: C 146 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7559 (mtp180) REVERT: C 250 SER cc_start: 0.8280 (p) cc_final: 0.7985 (m) REVERT: C 251 GLN cc_start: 0.7621 (mt0) cc_final: 0.7029 (mp10) REVERT: C 327 MET cc_start: 0.7482 (mtp) cc_final: 0.7213 (mtp) REVERT: C 359 ASN cc_start: 0.6722 (m110) cc_final: 0.5992 (t0) REVERT: D 3 SER cc_start: 0.8170 (t) cc_final: 0.7946 (p) REVERT: D 13 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6147 (mt-10) REVERT: D 47 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7296 (mttp) REVERT: D 73 GLN cc_start: 0.7128 (tt0) cc_final: 0.6843 (mt0) REVERT: D 84 MET cc_start: 0.7262 (mpp) cc_final: 0.6946 (tmm) REVERT: D 172 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6267 (mt-10) REVERT: D 185 ARG cc_start: 0.7756 (ptp-170) cc_final: 0.7472 (ptp-170) REVERT: D 255 ARG cc_start: 0.5664 (mtm110) cc_final: 0.5280 (mtt90) REVERT: E 45 ASP cc_start: 0.6705 (t70) cc_final: 0.6215 (m-30) REVERT: E 61 GLU cc_start: 0.7159 (tt0) cc_final: 0.6468 (pt0) REVERT: E 94 ARG cc_start: 0.7514 (mtp180) cc_final: 0.7024 (mtp180) REVERT: E 98 SER cc_start: 0.6909 (t) cc_final: 0.6552 (m) REVERT: F 58 GLN cc_start: 0.7455 (mp-120) cc_final: 0.6006 (tp-100) REVERT: F 74 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7204 (mp) REVERT: F 81 GLU cc_start: 0.6814 (mp0) cc_final: 0.5872 (mm-30) REVERT: F 83 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6890 (mt-10) REVERT: F 88 ARG cc_start: 0.7077 (ttt-90) cc_final: 0.6771 (ttt-90) REVERT: F 97 ARG cc_start: 0.7313 (mmm160) cc_final: 0.6940 (mmm160) REVERT: F 107 LYS cc_start: 0.7064 (mmmm) cc_final: 0.6770 (mttt) REVERT: F 148 GLU cc_start: 0.6678 (tt0) cc_final: 0.6362 (tt0) REVERT: G 20 ASP cc_start: 0.7947 (m-30) cc_final: 0.7574 (t0) REVERT: G 54 GLN cc_start: 0.6588 (mm-40) cc_final: 0.5773 (tm-30) REVERT: G 102 GLU cc_start: 0.6878 (tt0) cc_final: 0.6079 (mp0) REVERT: G 135 GLU cc_start: 0.6554 (tt0) cc_final: 0.6299 (tt0) REVERT: H 25 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: H 45 VAL cc_start: 0.7658 (m) cc_final: 0.7428 (t) REVERT: H 72 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: H 141 SER cc_start: 0.7786 (t) cc_final: 0.7467 (m) REVERT: H 187 ASP cc_start: 0.7056 (m-30) cc_final: 0.6765 (m-30) REVERT: H 191 LYS cc_start: 0.6507 (tttp) cc_final: 0.6216 (ttmt) REVERT: H 206 ARG cc_start: 0.6550 (ttm-80) cc_final: 0.5452 (ttm110) REVERT: H 225 ASN cc_start: 0.7571 (m-40) cc_final: 0.6996 (t0) REVERT: H 234 SER cc_start: 0.6967 (m) cc_final: 0.6663 (t) REVERT: H 269 MET cc_start: 0.8340 (ttm) cc_final: 0.8106 (ttm) REVERT: H 328 LYS cc_start: 0.6878 (mmmm) cc_final: 0.6660 (mppt) REVERT: I 25 ASP cc_start: 0.6914 (m-30) cc_final: 0.6597 (p0) REVERT: I 50 LYS cc_start: 0.7312 (mmpt) cc_final: 0.6954 (mtpt) REVERT: I 68 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7386 (mttt) REVERT: I 169 TYR cc_start: 0.6570 (m-80) cc_final: 0.5407 (t80) REVERT: I 215 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7316 (mttp) REVERT: I 305 MET cc_start: 0.8216 (mmm) cc_final: 0.7809 (mmm) REVERT: I 336 LYS cc_start: 0.6909 (ptpp) cc_final: 0.6634 (ttpt) REVERT: M 83 GLU cc_start: 0.6973 (tt0) cc_final: 0.6436 (tm-30) REVERT: M 194 THR cc_start: 0.8138 (m) cc_final: 0.7725 (p) REVERT: M 202 THR cc_start: 0.7850 (m) cc_final: 0.7604 (p) REVERT: M 206 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7186 (ttm110) REVERT: M 224 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7291 (pm20) REVERT: M 227 MET cc_start: 0.8362 (mmt) cc_final: 0.8029 (mmt) REVERT: N 41 GLN cc_start: 0.7083 (pt0) cc_final: 0.6834 (pm20) REVERT: N 47 MET cc_start: 0.1200 (ttp) cc_final: 0.0502 (ttm) REVERT: N 68 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7437 (mmtm) REVERT: N 211 ASP cc_start: 0.7576 (m-30) cc_final: 0.7274 (t70) REVERT: N 276 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6977 (mt-10) REVERT: N 299 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8337 (mtt) REVERT: N 328 LYS cc_start: 0.7492 (tptt) cc_final: 0.7066 (tptm) REVERT: N 360 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7215 (tp-100) REVERT: O 68 LYS cc_start: 0.7920 (ptmt) cc_final: 0.7630 (ptpp) REVERT: O 100 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7456 (mt-10) REVERT: O 113 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7030 (mmtp) REVERT: O 118 LYS cc_start: 0.7091 (mttm) cc_final: 0.6592 (mtpm) REVERT: O 206 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.6324 (ttp-110) REVERT: O 276 GLU cc_start: 0.6876 (tt0) cc_final: 0.6593 (tt0) REVERT: O 284 LYS cc_start: 0.7607 (mttm) cc_final: 0.7265 (mttm) REVERT: O 286 ASP cc_start: 0.6631 (t0) cc_final: 0.6347 (m-30) REVERT: O 326 LYS cc_start: 0.7240 (ptpp) cc_final: 0.6341 (mmmt) REVERT: O 328 LYS cc_start: 0.7772 (mtmt) cc_final: 0.6983 (tptm) REVERT: O 359 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7611 (tptp) REVERT: P 82 MET cc_start: 0.7874 (tpt) cc_final: 0.7260 (tpt) REVERT: P 355 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7884 (mtt) REVERT: P 359 LYS cc_start: 0.7266 (ptmm) cc_final: 0.6839 (tttt) REVERT: Q 6 THR cc_start: 0.8002 (p) cc_final: 0.7594 (t) REVERT: Q 34 ILE cc_start: 0.8432 (mt) cc_final: 0.8145 (pt) REVERT: Q 47 MET cc_start: 0.6300 (mmm) cc_final: 0.5426 (ptt) REVERT: Q 72 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: Q 190 MET cc_start: 0.7320 (mtm) cc_final: 0.6948 (mtp) REVERT: Q 246 GLN cc_start: 0.8112 (mt0) cc_final: 0.7749 (mt0) REVERT: Q 253 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: Q 291 LYS cc_start: 0.5449 (mttm) cc_final: 0.4705 (tmtm) REVERT: Q 313 MET cc_start: 0.7946 (tpt) cc_final: 0.7608 (mmm) REVERT: Q 328 LYS cc_start: 0.7391 (ttmt) cc_final: 0.6606 (ttpp) REVERT: Q 336 LYS cc_start: 0.7646 (tptm) cc_final: 0.7323 (tppt) REVERT: R 16 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7694 (mt) REVERT: R 99 GLU cc_start: 0.7266 (pt0) cc_final: 0.6940 (pm20) REVERT: R 125 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6713 (mp0) REVERT: R 206 ARG cc_start: 0.6679 (tpp80) cc_final: 0.6178 (ttm-80) REVERT: R 215 LYS cc_start: 0.7538 (mmmt) cc_final: 0.7246 (mptm) REVERT: R 225 ASN cc_start: 0.6562 (t0) cc_final: 0.6137 (m-40) REVERT: R 234 SER cc_start: 0.6016 (OUTLIER) cc_final: 0.5781 (t) REVERT: R 288 ASP cc_start: 0.7704 (p0) cc_final: 0.7398 (m-30) outliers start: 102 outliers final: 42 residues processed: 714 average time/residue: 2.8244 time to fit residues: 2458.5163 Evaluate side-chains 668 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 608 time to evaluate : 4.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain O residue 122 ILE Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 234 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 298 optimal weight: 2.9990 chunk 446 optimal weight: 0.0770 chunk 472 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 423 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 263 GLN D 254 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN R 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 39895 Z= 0.238 Angle : 0.609 7.346 54139 Z= 0.308 Chirality : 0.045 0.236 5990 Planarity : 0.005 0.062 6962 Dihedral : 9.484 160.451 5560 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.79 % Allowed : 14.65 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 4854 helix: 0.13 (0.12), residues: 1944 sheet: -0.54 (0.17), residues: 886 loop : 0.79 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 102 HIS 0.006 0.001 HIS O 161 PHE 0.018 0.001 PHE B 277 TYR 0.016 0.001 TYR B 88 ARG 0.007 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 741 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 624 time to evaluate : 4.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7325 (pt0) cc_final: 0.7050 (pp20) REVERT: A 137 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5925 (mp0) REVERT: A 207 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6589 (tppt) REVERT: A 226 ASP cc_start: 0.6621 (m-30) cc_final: 0.6317 (m-30) REVERT: A 239 ARG cc_start: 0.6027 (mtt180) cc_final: 0.5484 (mtm-85) REVERT: A 242 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.5912 (mp0) REVERT: A 253 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.6092 (mptt) REVERT: A 257 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6869 (ttt180) REVERT: A 302 ASP cc_start: 0.6643 (OUTLIER) cc_final: 0.6259 (m-30) REVERT: A 340 LYS cc_start: 0.7266 (tptp) cc_final: 0.6824 (ttpt) REVERT: A 356 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6732 (tm-30) REVERT: A 406 LYS cc_start: 0.6896 (pttp) cc_final: 0.6630 (ptpp) REVERT: B 6 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7435 (mt) REVERT: B 10 ASN cc_start: 0.7161 (p0) cc_final: 0.6932 (p0) REVERT: B 68 LYS cc_start: 0.6613 (mtmt) cc_final: 0.6160 (mtmt) REVERT: B 73 ASN cc_start: 0.7438 (m-40) cc_final: 0.6977 (t0) REVERT: B 96 ILE cc_start: 0.7793 (mm) cc_final: 0.7420 (pt) REVERT: B 119 MET cc_start: 0.6543 (ttm) cc_final: 0.6342 (ttp) REVERT: B 152 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7857 (p) REVERT: B 228 LYS cc_start: 0.6527 (ttpt) cc_final: 0.5856 (ttpp) REVERT: B 295 ARG cc_start: 0.6642 (mtp180) cc_final: 0.5651 (mpt-90) REVERT: B 364 ASN cc_start: 0.7183 (m-40) cc_final: 0.6717 (t0) REVERT: C 22 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7276 (mp10) REVERT: C 41 ASP cc_start: 0.6157 (t0) cc_final: 0.5580 (p0) REVERT: C 83 GLU cc_start: 0.6974 (tt0) cc_final: 0.6184 (mp0) REVERT: C 91 LYS cc_start: 0.7421 (ttpt) cc_final: 0.5982 (tptp) REVERT: C 251 GLN cc_start: 0.7503 (mt0) cc_final: 0.6920 (mp10) REVERT: C 276 LEU cc_start: 0.7122 (tp) cc_final: 0.6826 (tm) REVERT: C 327 MET cc_start: 0.7474 (mtp) cc_final: 0.7229 (mtm) REVERT: C 359 ASN cc_start: 0.6726 (m110) cc_final: 0.5997 (t0) REVERT: D 3 SER cc_start: 0.8227 (t) cc_final: 0.7969 (p) REVERT: D 13 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6131 (mt-10) REVERT: D 47 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7251 (mttp) REVERT: D 73 GLN cc_start: 0.7138 (tt0) cc_final: 0.6818 (mt0) REVERT: D 84 MET cc_start: 0.7261 (mpp) cc_final: 0.6966 (tmm) REVERT: D 113 MET cc_start: 0.6890 (mmt) cc_final: 0.6430 (mmt) REVERT: D 172 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6332 (mt-10) REVERT: D 185 ARG cc_start: 0.7738 (ptp-170) cc_final: 0.7428 (ptp-170) REVERT: D 255 ARG cc_start: 0.5733 (mtm110) cc_final: 0.5324 (mtt90) REVERT: E 58 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6916 (ptm160) REVERT: E 61 GLU cc_start: 0.7212 (tt0) cc_final: 0.6428 (pt0) REVERT: E 94 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7036 (mtp180) REVERT: E 98 SER cc_start: 0.6839 (t) cc_final: 0.6493 (m) REVERT: F 23 GLU cc_start: 0.7514 (tt0) cc_final: 0.7170 (tt0) REVERT: F 58 GLN cc_start: 0.7461 (mp-120) cc_final: 0.6088 (tp-100) REVERT: F 74 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7229 (mp) REVERT: F 81 GLU cc_start: 0.6909 (mp0) cc_final: 0.5919 (mm-30) REVERT: F 88 ARG cc_start: 0.7077 (ttt-90) cc_final: 0.5871 (ttm110) REVERT: F 97 ARG cc_start: 0.7289 (mmm160) cc_final: 0.6927 (mmm160) REVERT: F 107 LYS cc_start: 0.7031 (mmmm) cc_final: 0.6752 (mttt) REVERT: F 119 THR cc_start: 0.7365 (m) cc_final: 0.6994 (p) REVERT: F 148 GLU cc_start: 0.6751 (tt0) cc_final: 0.6395 (tt0) REVERT: G 20 ASP cc_start: 0.8046 (m-30) cc_final: 0.7596 (t0) REVERT: G 54 GLN cc_start: 0.6635 (mm-40) cc_final: 0.5828 (tm-30) REVERT: G 135 GLU cc_start: 0.6549 (tt0) cc_final: 0.6309 (tt0) REVERT: H 25 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: H 28 ARG cc_start: 0.7694 (tpp-160) cc_final: 0.7308 (tpp80) REVERT: H 72 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: H 141 SER cc_start: 0.7758 (t) cc_final: 0.7408 (m) REVERT: H 187 ASP cc_start: 0.7125 (m-30) cc_final: 0.6836 (m-30) REVERT: H 191 LYS cc_start: 0.6570 (tttp) cc_final: 0.6228 (ttmt) REVERT: H 206 ARG cc_start: 0.6597 (ttm-80) cc_final: 0.5504 (ttm110) REVERT: H 225 ASN cc_start: 0.7536 (m-40) cc_final: 0.6909 (t0) REVERT: H 234 SER cc_start: 0.6984 (m) cc_final: 0.6683 (t) REVERT: H 269 MET cc_start: 0.8354 (ttm) cc_final: 0.8142 (ttp) REVERT: H 306 TYR cc_start: 0.8750 (m-80) cc_final: 0.8416 (m-80) REVERT: I 25 ASP cc_start: 0.6899 (m-30) cc_final: 0.6594 (p0) REVERT: I 50 LYS cc_start: 0.7291 (mmpt) cc_final: 0.6960 (mtpt) REVERT: I 68 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7396 (mttt) REVERT: I 183 ARG cc_start: 0.7096 (tpp80) cc_final: 0.6886 (tpp80) REVERT: I 215 LYS cc_start: 0.7686 (mtpp) cc_final: 0.7321 (mttp) REVERT: I 305 MET cc_start: 0.8225 (mmm) cc_final: 0.7734 (mmm) REVERT: I 336 LYS cc_start: 0.6881 (ptpp) cc_final: 0.6564 (ttpt) REVERT: M 78 ASN cc_start: 0.7417 (t0) cc_final: 0.6945 (t0) REVERT: M 194 THR cc_start: 0.8147 (m) cc_final: 0.7762 (p) REVERT: M 202 THR cc_start: 0.7934 (m) cc_final: 0.7705 (p) REVERT: M 206 ARG cc_start: 0.7850 (ttm110) cc_final: 0.7324 (ttm110) REVERT: M 224 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7282 (pm20) REVERT: M 227 MET cc_start: 0.8356 (mmt) cc_final: 0.7974 (mmt) REVERT: M 355 MET cc_start: 0.7561 (mtp) cc_final: 0.7342 (mtp) REVERT: N 47 MET cc_start: 0.1211 (ttp) cc_final: 0.0490 (ttm) REVERT: N 211 ASP cc_start: 0.7593 (m-30) cc_final: 0.7307 (t70) REVERT: N 276 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6991 (mt-10) REVERT: N 328 LYS cc_start: 0.7464 (tptt) cc_final: 0.7069 (tptm) REVERT: N 355 MET cc_start: 0.7827 (mtp) cc_final: 0.7448 (mtt) REVERT: N 360 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7178 (tp-100) REVERT: O 34 ILE cc_start: 0.8714 (mt) cc_final: 0.8156 (pt) REVERT: O 68 LYS cc_start: 0.7970 (ptmt) cc_final: 0.7690 (ptpp) REVERT: O 100 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7436 (mt-10) REVERT: O 113 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6832 (mttt) REVERT: O 206 ARG cc_start: 0.7452 (ttp-170) cc_final: 0.6250 (ttm-80) REVERT: O 276 GLU cc_start: 0.6908 (tt0) cc_final: 0.6640 (tt0) REVERT: O 284 LYS cc_start: 0.7686 (mttm) cc_final: 0.7385 (mtpm) REVERT: O 286 ASP cc_start: 0.6696 (t0) cc_final: 0.6339 (m-30) REVERT: O 326 LYS cc_start: 0.7373 (ptpp) cc_final: 0.6495 (mmmt) REVERT: O 328 LYS cc_start: 0.7820 (mtmt) cc_final: 0.6967 (tptm) REVERT: O 359 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7656 (tptp) REVERT: P 82 MET cc_start: 0.7886 (tpt) cc_final: 0.7262 (tpt) REVERT: P 120 THR cc_start: 0.7645 (t) cc_final: 0.7342 (p) REVERT: P 141 SER cc_start: 0.7931 (t) cc_final: 0.7601 (m) REVERT: P 355 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7835 (mtt) REVERT: P 359 LYS cc_start: 0.7249 (ptmm) cc_final: 0.6834 (tttt) REVERT: Q 6 THR cc_start: 0.7974 (p) cc_final: 0.7529 (t) REVERT: Q 34 ILE cc_start: 0.8417 (mt) cc_final: 0.8172 (pt) REVERT: Q 47 MET cc_start: 0.6397 (mmm) cc_final: 0.5468 (ptt) REVERT: Q 61 LYS cc_start: 0.7393 (mtpp) cc_final: 0.7166 (mttp) REVERT: Q 72 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: Q 190 MET cc_start: 0.7376 (mtm) cc_final: 0.7067 (mtp) REVERT: Q 253 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: Q 291 LYS cc_start: 0.5367 (mttm) cc_final: 0.4658 (tmtm) REVERT: Q 313 MET cc_start: 0.7996 (tpt) cc_final: 0.7645 (mmm) REVERT: Q 328 LYS cc_start: 0.7324 (ttmt) cc_final: 0.6535 (ttpp) REVERT: Q 336 LYS cc_start: 0.7678 (tptm) cc_final: 0.7349 (tppt) REVERT: R 16 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7671 (mt) REVERT: R 72 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6957 (mt-10) REVERT: R 99 GLU cc_start: 0.7278 (pt0) cc_final: 0.6939 (pm20) REVERT: R 206 ARG cc_start: 0.6744 (tpp80) cc_final: 0.6112 (ttm-80) REVERT: R 215 LYS cc_start: 0.7549 (mmmt) cc_final: 0.7271 (mptm) REVERT: R 225 ASN cc_start: 0.6544 (t0) cc_final: 0.6120 (m-40) outliers start: 117 outliers final: 45 residues processed: 696 average time/residue: 2.7959 time to fit residues: 2368.1971 Evaluate side-chains 657 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 595 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 351 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 403 optimal weight: 1.9990 chunk 326 optimal weight: 0.0060 chunk 0 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 424 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 160 HIS ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN N 296 ASN ** O 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 ASN Q 41 GLN R 137 GLN R 275 HIS R 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39895 Z= 0.283 Angle : 0.619 7.820 54139 Z= 0.311 Chirality : 0.045 0.213 5990 Planarity : 0.005 0.109 6962 Dihedral : 9.252 169.780 5555 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.57 % Allowed : 15.44 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.12), residues: 4854 helix: 0.23 (0.12), residues: 1945 sheet: -0.32 (0.16), residues: 937 loop : 0.74 (0.15), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 102 HIS 0.008 0.001 HIS O 161 PHE 0.017 0.001 PHE B 277 TYR 0.029 0.001 TYR A 402 ARG 0.013 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 709 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 601 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7313 (pt0) cc_final: 0.6994 (pp20) REVERT: A 137 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5841 (mp0) REVERT: A 207 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6611 (tppt) REVERT: A 226 ASP cc_start: 0.6607 (m-30) cc_final: 0.6331 (m-30) REVERT: A 239 ARG cc_start: 0.5841 (mtt180) cc_final: 0.5382 (mtm-85) REVERT: A 242 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: A 253 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.6093 (mptt) REVERT: A 302 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6427 (m-30) REVERT: A 340 LYS cc_start: 0.7184 (tptp) cc_final: 0.6776 (ttpt) REVERT: A 356 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6763 (tm-30) REVERT: A 406 LYS cc_start: 0.6893 (pttp) cc_final: 0.6503 (ptpt) REVERT: B 10 ASN cc_start: 0.7180 (p0) cc_final: 0.6947 (p0) REVERT: B 68 LYS cc_start: 0.6635 (mtmt) cc_final: 0.6115 (mtmt) REVERT: B 73 ASN cc_start: 0.7544 (m-40) cc_final: 0.7070 (t0) REVERT: B 96 ILE cc_start: 0.7849 (mm) cc_final: 0.7422 (pt) REVERT: B 228 LYS cc_start: 0.6626 (ttpt) cc_final: 0.5921 (ttpp) REVERT: B 295 ARG cc_start: 0.6673 (mtp180) cc_final: 0.5581 (mpt-90) REVERT: B 364 ASN cc_start: 0.7253 (m-40) cc_final: 0.6759 (t0) REVERT: C 22 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7314 (mp10) REVERT: C 83 GLU cc_start: 0.6981 (tt0) cc_final: 0.6214 (mp0) REVERT: C 91 LYS cc_start: 0.7442 (ttpt) cc_final: 0.5981 (tptp) REVERT: C 251 GLN cc_start: 0.7541 (mt0) cc_final: 0.6997 (mp10) REVERT: C 359 ASN cc_start: 0.6754 (m110) cc_final: 0.6015 (t0) REVERT: D 3 SER cc_start: 0.8227 (t) cc_final: 0.7950 (p) REVERT: D 13 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6140 (mt-10) REVERT: D 47 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7290 (mttp) REVERT: D 73 GLN cc_start: 0.7071 (tt0) cc_final: 0.6817 (mt0) REVERT: D 84 MET cc_start: 0.7192 (mpp) cc_final: 0.6900 (tmm) REVERT: D 102 GLU cc_start: 0.6557 (mp0) cc_final: 0.6336 (mp0) REVERT: D 106 GLN cc_start: 0.6295 (pt0) cc_final: 0.5924 (mt0) REVERT: D 165 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6739 (mm-30) REVERT: D 172 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6529 (mt-10) REVERT: D 185 ARG cc_start: 0.7747 (ptp-170) cc_final: 0.7371 (ptp-170) REVERT: D 255 ARG cc_start: 0.5866 (mtm110) cc_final: 0.5321 (mtt90) REVERT: E 58 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6960 (ptm160) REVERT: E 61 GLU cc_start: 0.7304 (tt0) cc_final: 0.6509 (pt0) REVERT: E 94 ARG cc_start: 0.7532 (mtp180) cc_final: 0.7053 (mtp180) REVERT: E 98 SER cc_start: 0.6835 (t) cc_final: 0.6498 (m) REVERT: F 23 GLU cc_start: 0.7553 (tt0) cc_final: 0.7179 (tt0) REVERT: F 58 GLN cc_start: 0.7548 (mp-120) cc_final: 0.6231 (tp-100) REVERT: F 81 GLU cc_start: 0.6890 (mp0) cc_final: 0.5896 (mm-30) REVERT: F 97 ARG cc_start: 0.7300 (mmm160) cc_final: 0.6936 (mmm160) REVERT: F 107 LYS cc_start: 0.7060 (mmmm) cc_final: 0.6736 (mttt) REVERT: F 119 THR cc_start: 0.7385 (m) cc_final: 0.7082 (p) REVERT: G 54 GLN cc_start: 0.6621 (mm-40) cc_final: 0.5819 (tm-30) REVERT: G 98 GLU cc_start: 0.7060 (pp20) cc_final: 0.6846 (pp20) REVERT: G 135 GLU cc_start: 0.6629 (tt0) cc_final: 0.6400 (tt0) REVERT: H 25 ASP cc_start: 0.8301 (p0) cc_final: 0.7563 (m-30) REVERT: H 28 ARG cc_start: 0.7702 (tpp-160) cc_final: 0.7341 (tpp80) REVERT: H 68 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7472 (mttm) REVERT: H 72 GLU cc_start: 0.6734 (tt0) cc_final: 0.6238 (mp0) REVERT: H 141 SER cc_start: 0.7787 (t) cc_final: 0.7424 (m) REVERT: H 187 ASP cc_start: 0.7268 (m-30) cc_final: 0.6990 (m-30) REVERT: H 191 LYS cc_start: 0.6687 (tttp) cc_final: 0.6317 (ttpt) REVERT: H 206 ARG cc_start: 0.6667 (ttm-80) cc_final: 0.5951 (ttp-170) REVERT: H 225 ASN cc_start: 0.7561 (m-40) cc_final: 0.6893 (t0) REVERT: H 234 SER cc_start: 0.6916 (m) cc_final: 0.6614 (t) REVERT: H 306 TYR cc_start: 0.8794 (m-80) cc_final: 0.8476 (m-80) REVERT: I 50 LYS cc_start: 0.7292 (mmpt) cc_final: 0.6982 (mtpt) REVERT: I 68 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7459 (mttt) REVERT: I 123 MET cc_start: 0.7192 (tpt) cc_final: 0.6977 (tpt) REVERT: I 215 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7257 (mttp) REVERT: I 305 MET cc_start: 0.8291 (mmm) cc_final: 0.7910 (mmm) REVERT: M 194 THR cc_start: 0.8114 (m) cc_final: 0.7791 (p) REVERT: M 202 THR cc_start: 0.7934 (m) cc_final: 0.7685 (p) REVERT: M 224 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7294 (pm20) REVERT: M 263 GLN cc_start: 0.7661 (mt0) cc_final: 0.7338 (mt0) REVERT: N 47 MET cc_start: 0.1198 (ttp) cc_final: 0.0454 (ttm) REVERT: N 206 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6664 (ttm110) REVERT: N 211 ASP cc_start: 0.7567 (m-30) cc_final: 0.7315 (t70) REVERT: N 305 MET cc_start: 0.8189 (mtp) cc_final: 0.7757 (mmt) REVERT: N 328 LYS cc_start: 0.7473 (tptt) cc_final: 0.7065 (tptm) REVERT: N 355 MET cc_start: 0.7821 (mtp) cc_final: 0.7495 (mtp) REVERT: N 360 GLN cc_start: 0.7382 (tm-30) cc_final: 0.7176 (tp-100) REVERT: O 68 LYS cc_start: 0.7981 (ptmt) cc_final: 0.7679 (ptpp) REVERT: O 100 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7540 (mt-10) REVERT: O 113 LYS cc_start: 0.7468 (mmtt) cc_final: 0.6876 (mttt) REVERT: O 206 ARG cc_start: 0.7446 (ttp-170) cc_final: 0.6256 (ttm-80) REVERT: O 276 GLU cc_start: 0.6913 (tt0) cc_final: 0.6655 (tt0) REVERT: O 284 LYS cc_start: 0.7777 (mttm) cc_final: 0.7436 (mtpm) REVERT: O 326 LYS cc_start: 0.7517 (ptpp) cc_final: 0.6646 (mmmt) REVERT: O 328 LYS cc_start: 0.7828 (mtmt) cc_final: 0.6921 (tptm) REVERT: O 359 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7660 (tptp) REVERT: P 82 MET cc_start: 0.7910 (tpt) cc_final: 0.7340 (tpt) REVERT: P 120 THR cc_start: 0.7702 (t) cc_final: 0.7412 (p) REVERT: P 141 SER cc_start: 0.7971 (t) cc_final: 0.7613 (m) REVERT: P 224 GLU cc_start: 0.7135 (tp30) cc_final: 0.6915 (mm-30) REVERT: P 355 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7799 (mtt) REVERT: P 359 LYS cc_start: 0.7274 (ptmm) cc_final: 0.6819 (tptt) REVERT: Q 6 THR cc_start: 0.7955 (p) cc_final: 0.7454 (t) REVERT: Q 34 ILE cc_start: 0.8421 (mt) cc_final: 0.8161 (pt) REVERT: Q 47 MET cc_start: 0.6505 (mmm) cc_final: 0.5537 (ptt) REVERT: Q 61 LYS cc_start: 0.7460 (mtpp) cc_final: 0.7228 (mttp) REVERT: Q 72 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: Q 190 MET cc_start: 0.7370 (mtm) cc_final: 0.7031 (mtp) REVERT: Q 225 ASN cc_start: 0.7128 (t0) cc_final: 0.6670 (m110) REVERT: Q 291 LYS cc_start: 0.5352 (mttm) cc_final: 0.4702 (tmtm) REVERT: Q 313 MET cc_start: 0.8000 (tpt) cc_final: 0.7667 (mmm) REVERT: Q 328 LYS cc_start: 0.7379 (ttmt) cc_final: 0.6627 (ttmt) REVERT: Q 336 LYS cc_start: 0.7692 (tptm) cc_final: 0.7411 (tttt) REVERT: R 72 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6983 (mt-10) REVERT: R 99 GLU cc_start: 0.7271 (pt0) cc_final: 0.6984 (pm20) REVERT: R 107 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.6215 (tp30) REVERT: R 206 ARG cc_start: 0.6812 (tpp80) cc_final: 0.6222 (ttm-80) REVERT: R 215 LYS cc_start: 0.7530 (mmmt) cc_final: 0.7240 (mptm) REVERT: R 225 ASN cc_start: 0.6613 (t0) cc_final: 0.6122 (m-40) REVERT: R 314 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: R 358 THR cc_start: 0.7778 (m) cc_final: 0.7441 (p) outliers start: 108 outliers final: 48 residues processed: 671 average time/residue: 2.8776 time to fit residues: 2351.1870 Evaluate side-chains 636 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 574 time to evaluate : 4.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 314 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 159 optimal weight: 9.9990 chunk 425 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 277 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 473 optimal weight: 2.9990 chunk 392 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 39 optimal weight: 0.0870 chunk 156 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN G 19 GLN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 GLN O 162 ASN O 225 ASN Q 41 GLN R 137 GLN R 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 39895 Z= 0.272 Angle : 0.606 7.721 54139 Z= 0.304 Chirality : 0.045 0.212 5990 Planarity : 0.005 0.094 6962 Dihedral : 9.072 174.841 5549 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.45 % Allowed : 16.17 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.12), residues: 4854 helix: 0.29 (0.12), residues: 1945 sheet: -0.30 (0.16), residues: 945 loop : 0.73 (0.15), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 102 HIS 0.006 0.001 HIS O 161 PHE 0.016 0.001 PHE B 277 TYR 0.027 0.001 TYR B 377 ARG 0.009 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 687 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 584 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7309 (pt0) cc_final: 0.6955 (pp20) REVERT: A 137 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.5864 (mp0) REVERT: A 207 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6653 (tppt) REVERT: A 226 ASP cc_start: 0.6607 (m-30) cc_final: 0.6273 (m-30) REVERT: A 239 ARG cc_start: 0.5811 (mtt180) cc_final: 0.5393 (mtm-85) REVERT: A 242 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5943 (mp0) REVERT: A 253 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6088 (mptt) REVERT: A 257 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6931 (ttt180) REVERT: A 302 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6458 (m-30) REVERT: A 340 LYS cc_start: 0.7208 (tptp) cc_final: 0.6767 (ttpt) REVERT: A 356 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6840 (tm-30) REVERT: A 402 TYR cc_start: 0.7397 (m-80) cc_final: 0.6938 (m-80) REVERT: A 406 LYS cc_start: 0.6940 (pttp) cc_final: 0.6503 (ptpt) REVERT: B 21 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7366 (mtmm) REVERT: B 68 LYS cc_start: 0.6667 (mtmt) cc_final: 0.6146 (mtmt) REVERT: B 73 ASN cc_start: 0.7579 (m-40) cc_final: 0.7101 (t0) REVERT: B 96 ILE cc_start: 0.7878 (mm) cc_final: 0.7413 (pt) REVERT: B 228 LYS cc_start: 0.6688 (ttpt) cc_final: 0.5970 (ttpp) REVERT: B 295 ARG cc_start: 0.6653 (mtp180) cc_final: 0.5540 (mpt-90) REVERT: B 364 ASN cc_start: 0.7237 (m-40) cc_final: 0.6724 (t0) REVERT: C 22 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7307 (mp10) REVERT: C 83 GLU cc_start: 0.7010 (tt0) cc_final: 0.6270 (mp0) REVERT: C 91 LYS cc_start: 0.7469 (ttpt) cc_final: 0.5998 (tptp) REVERT: C 251 GLN cc_start: 0.7443 (mt0) cc_final: 0.6972 (mp10) REVERT: C 359 ASN cc_start: 0.6757 (m110) cc_final: 0.6010 (t0) REVERT: D 3 SER cc_start: 0.8231 (t) cc_final: 0.8000 (m) REVERT: D 13 GLU cc_start: 0.6558 (mm-30) cc_final: 0.6139 (mt-10) REVERT: D 47 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7205 (mttp) REVERT: D 73 GLN cc_start: 0.7056 (tt0) cc_final: 0.6813 (mt0) REVERT: D 84 MET cc_start: 0.7175 (mpp) cc_final: 0.6891 (tmm) REVERT: D 102 GLU cc_start: 0.6561 (mp0) cc_final: 0.6326 (mp0) REVERT: D 106 GLN cc_start: 0.6216 (pt0) cc_final: 0.5902 (mt0) REVERT: D 163 ASP cc_start: 0.6607 (p0) cc_final: 0.6140 (p0) REVERT: D 172 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6561 (mt-10) REVERT: D 185 ARG cc_start: 0.7706 (ptp-170) cc_final: 0.7350 (ptp-170) REVERT: D 255 ARG cc_start: 0.5896 (mtm110) cc_final: 0.5336 (mtt90) REVERT: D 269 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6460 (mp) REVERT: D 287 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5329 (mtp180) REVERT: E 58 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6949 (ptm160) REVERT: E 94 ARG cc_start: 0.7549 (mtp180) cc_final: 0.7069 (mtp180) REVERT: E 98 SER cc_start: 0.6855 (t) cc_final: 0.6507 (m) REVERT: F 56 ASN cc_start: 0.7116 (m-40) cc_final: 0.6462 (m110) REVERT: F 58 GLN cc_start: 0.7544 (mp-120) cc_final: 0.6204 (tp-100) REVERT: F 81 GLU cc_start: 0.6942 (mp0) cc_final: 0.5900 (mm-30) REVERT: F 97 ARG cc_start: 0.7295 (mmm160) cc_final: 0.6931 (mmm160) REVERT: F 107 LYS cc_start: 0.7052 (mmmm) cc_final: 0.6731 (mttt) REVERT: F 119 THR cc_start: 0.7317 (m) cc_final: 0.7014 (p) REVERT: F 145 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5387 (mm-30) REVERT: F 148 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: G 135 GLU cc_start: 0.6619 (tt0) cc_final: 0.6390 (tt0) REVERT: H 25 ASP cc_start: 0.8258 (p0) cc_final: 0.7496 (m-30) REVERT: H 28 ARG cc_start: 0.7680 (tpp-160) cc_final: 0.7348 (tpp80) REVERT: H 68 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7498 (mttm) REVERT: H 72 GLU cc_start: 0.6745 (tt0) cc_final: 0.6249 (mp0) REVERT: H 141 SER cc_start: 0.7818 (t) cc_final: 0.7434 (m) REVERT: H 191 LYS cc_start: 0.6715 (tttp) cc_final: 0.6331 (ttpt) REVERT: H 206 ARG cc_start: 0.6638 (ttm-80) cc_final: 0.5562 (ttm110) REVERT: H 225 ASN cc_start: 0.7573 (m-40) cc_final: 0.6896 (t0) REVERT: H 234 SER cc_start: 0.6918 (m) cc_final: 0.6616 (t) REVERT: H 306 TYR cc_start: 0.8822 (m-80) cc_final: 0.8450 (m-80) REVERT: I 50 LYS cc_start: 0.7267 (mmpt) cc_final: 0.6927 (mtpt) REVERT: I 68 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7467 (mttt) REVERT: I 95 ARG cc_start: 0.7132 (mtp85) cc_final: 0.6870 (mtt-85) REVERT: I 215 LYS cc_start: 0.7683 (mtpp) cc_final: 0.7265 (mttp) REVERT: I 305 MET cc_start: 0.8333 (mmm) cc_final: 0.7955 (mmm) REVERT: M 194 THR cc_start: 0.8133 (m) cc_final: 0.7838 (p) REVERT: M 202 THR cc_start: 0.7945 (m) cc_final: 0.7720 (p) REVERT: M 224 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7283 (pm20) REVERT: N 47 MET cc_start: 0.1225 (ttp) cc_final: 0.0479 (ttm) REVERT: N 206 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6656 (ttm110) REVERT: N 211 ASP cc_start: 0.7587 (m-30) cc_final: 0.7333 (t70) REVERT: N 236 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7683 (mp) REVERT: N 328 LYS cc_start: 0.7494 (tptt) cc_final: 0.7076 (tptm) REVERT: N 355 MET cc_start: 0.7824 (mtp) cc_final: 0.7400 (mtt) REVERT: O 68 LYS cc_start: 0.7998 (ptmt) cc_final: 0.7677 (ptpp) REVERT: O 72 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: O 100 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7524 (mt-10) REVERT: O 113 LYS cc_start: 0.7451 (mmtt) cc_final: 0.6876 (mttt) REVERT: O 206 ARG cc_start: 0.7450 (ttp-170) cc_final: 0.6269 (ttp-110) REVERT: O 248 ILE cc_start: 0.7732 (mp) cc_final: 0.7508 (pp) REVERT: O 276 GLU cc_start: 0.6989 (tt0) cc_final: 0.6726 (tt0) REVERT: O 284 LYS cc_start: 0.7758 (mttm) cc_final: 0.7413 (mtpm) REVERT: O 326 LYS cc_start: 0.7539 (ptpp) cc_final: 0.6658 (mmmt) REVERT: O 328 LYS cc_start: 0.7845 (mtmt) cc_final: 0.6908 (tptm) REVERT: O 359 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7662 (tptp) REVERT: P 82 MET cc_start: 0.7901 (tpt) cc_final: 0.7345 (tpt) REVERT: P 120 THR cc_start: 0.7675 (t) cc_final: 0.7439 (p) REVERT: P 141 SER cc_start: 0.7969 (t) cc_final: 0.7633 (m) REVERT: P 206 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6305 (ttm110) REVERT: P 224 GLU cc_start: 0.7157 (tp30) cc_final: 0.6930 (mm-30) REVERT: P 355 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8002 (mpp) REVERT: P 359 LYS cc_start: 0.7279 (ptmm) cc_final: 0.6825 (tptt) REVERT: Q 6 THR cc_start: 0.7949 (p) cc_final: 0.7435 (t) REVERT: Q 34 ILE cc_start: 0.8423 (mt) cc_final: 0.8147 (pt) REVERT: Q 47 MET cc_start: 0.6579 (mmm) cc_final: 0.5591 (ptt) REVERT: Q 61 LYS cc_start: 0.7454 (mtpp) cc_final: 0.7232 (mttp) REVERT: Q 72 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6653 (mt-10) REVERT: Q 82 MET cc_start: 0.8227 (tpt) cc_final: 0.7768 (tpt) REVERT: Q 190 MET cc_start: 0.7398 (mtm) cc_final: 0.7120 (mtp) REVERT: Q 291 LYS cc_start: 0.5411 (mttm) cc_final: 0.4760 (tmtm) REVERT: Q 313 MET cc_start: 0.8019 (tpt) cc_final: 0.7714 (mmm) REVERT: Q 328 LYS cc_start: 0.7385 (ttmt) cc_final: 0.6633 (ttmt) REVERT: Q 336 LYS cc_start: 0.7713 (tptm) cc_final: 0.7418 (ttmt) REVERT: Q 354 GLN cc_start: 0.7795 (pm20) cc_final: 0.7274 (mm110) REVERT: R 72 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7001 (mt-10) REVERT: R 99 GLU cc_start: 0.7284 (pt0) cc_final: 0.7012 (pm20) REVERT: R 107 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.6248 (tp30) REVERT: R 206 ARG cc_start: 0.6806 (tpp80) cc_final: 0.6206 (ttm-80) REVERT: R 215 LYS cc_start: 0.7521 (mmmt) cc_final: 0.7248 (mptm) REVERT: R 225 ASN cc_start: 0.6613 (t0) cc_final: 0.6114 (m-40) REVERT: R 358 THR cc_start: 0.7770 (m) cc_final: 0.7467 (p) outliers start: 103 outliers final: 55 residues processed: 653 average time/residue: 2.8559 time to fit residues: 2270.9175 Evaluate side-chains 647 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 572 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 456 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 398 optimal weight: 0.9990 chunk 264 optimal weight: 0.4980 chunk 471 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 360 GLN O 225 ASN Q 162 ASN R 137 GLN R 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39895 Z= 0.220 Angle : 0.582 7.616 54139 Z= 0.289 Chirality : 0.044 0.219 5990 Planarity : 0.004 0.085 6962 Dihedral : 8.772 174.098 5548 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.38 % Allowed : 16.41 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.12), residues: 4854 helix: 0.42 (0.12), residues: 1945 sheet: -0.32 (0.16), residues: 953 loop : 0.80 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 102 HIS 0.010 0.001 HIS I 173 PHE 0.015 0.001 PHE B 277 TYR 0.018 0.001 TYR I 279 ARG 0.012 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 696 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 596 time to evaluate : 4.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7278 (pt0) cc_final: 0.6968 (pp20) REVERT: A 137 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: A 207 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6659 (tppt) REVERT: A 226 ASP cc_start: 0.6581 (m-30) cc_final: 0.6306 (m-30) REVERT: A 239 ARG cc_start: 0.5806 (mtt180) cc_final: 0.5368 (mtm-85) REVERT: A 242 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: A 253 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6104 (mptt) REVERT: A 302 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6547 (m-30) REVERT: A 340 LYS cc_start: 0.7171 (tptp) cc_final: 0.6729 (ttpt) REVERT: A 356 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6830 (tm-30) REVERT: A 365 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.7711 (p) REVERT: A 402 TYR cc_start: 0.7453 (m-80) cc_final: 0.6970 (m-80) REVERT: A 406 LYS cc_start: 0.6909 (pttp) cc_final: 0.6511 (ptpt) REVERT: B 68 LYS cc_start: 0.6662 (mtmt) cc_final: 0.6236 (mtmt) REVERT: B 73 ASN cc_start: 0.7569 (m-40) cc_final: 0.7103 (t0) REVERT: B 96 ILE cc_start: 0.7847 (mm) cc_final: 0.7457 (pt) REVERT: B 228 LYS cc_start: 0.6696 (ttpt) cc_final: 0.5988 (ttpp) REVERT: B 295 ARG cc_start: 0.6676 (mtp180) cc_final: 0.5549 (mpt-90) REVERT: B 300 SER cc_start: 0.7672 (t) cc_final: 0.7289 (p) REVERT: B 364 ASN cc_start: 0.7237 (m-40) cc_final: 0.6708 (t0) REVERT: C 22 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7290 (mp10) REVERT: C 52 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8155 (m) REVERT: C 83 GLU cc_start: 0.7007 (tt0) cc_final: 0.6256 (mp0) REVERT: C 91 LYS cc_start: 0.7500 (ttpt) cc_final: 0.6012 (tptp) REVERT: C 251 GLN cc_start: 0.7469 (mt0) cc_final: 0.7001 (mp10) REVERT: C 359 ASN cc_start: 0.6768 (m110) cc_final: 0.6001 (t0) REVERT: D 3 SER cc_start: 0.8222 (t) cc_final: 0.7997 (m) REVERT: D 13 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6103 (mt-10) REVERT: D 47 LYS cc_start: 0.7734 (mtmm) cc_final: 0.7134 (mttp) REVERT: D 73 GLN cc_start: 0.7065 (tt0) cc_final: 0.6773 (mt0) REVERT: D 84 MET cc_start: 0.7174 (mpp) cc_final: 0.6887 (tmm) REVERT: D 102 GLU cc_start: 0.6615 (mp0) cc_final: 0.6088 (mp0) REVERT: D 143 ASN cc_start: 0.6870 (OUTLIER) cc_final: 0.6454 (t0) REVERT: D 172 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6626 (mt-10) REVERT: D 185 ARG cc_start: 0.7699 (ptp-170) cc_final: 0.7387 (ptp-170) REVERT: D 186 GLU cc_start: 0.6349 (tp30) cc_final: 0.6110 (tp30) REVERT: D 255 ARG cc_start: 0.5934 (mtm110) cc_final: 0.5347 (mtt90) REVERT: D 287 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.5354 (mtp180) REVERT: E 58 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7030 (ptm160) REVERT: E 94 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7108 (mtp180) REVERT: E 98 SER cc_start: 0.6856 (t) cc_final: 0.6508 (m) REVERT: F 23 GLU cc_start: 0.7607 (tt0) cc_final: 0.7227 (tt0) REVERT: F 58 GLN cc_start: 0.7477 (mp-120) cc_final: 0.6051 (tp-100) REVERT: F 81 GLU cc_start: 0.6916 (mp0) cc_final: 0.5863 (mm-30) REVERT: F 97 ARG cc_start: 0.7332 (mmm160) cc_final: 0.6979 (mmm160) REVERT: F 107 LYS cc_start: 0.7043 (mmmm) cc_final: 0.6738 (mttt) REVERT: F 119 THR cc_start: 0.7312 (m) cc_final: 0.7024 (p) REVERT: F 145 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5314 (mm-30) REVERT: F 148 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6550 (tt0) REVERT: G 132 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6424 (mppt) REVERT: G 135 GLU cc_start: 0.6582 (tt0) cc_final: 0.6369 (tt0) REVERT: H 25 ASP cc_start: 0.8279 (p0) cc_final: 0.7486 (m-30) REVERT: H 28 ARG cc_start: 0.7681 (tpp-160) cc_final: 0.7362 (tpp80) REVERT: H 68 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7514 (mttm) REVERT: H 72 GLU cc_start: 0.6752 (tt0) cc_final: 0.6263 (mp0) REVERT: H 141 SER cc_start: 0.7766 (t) cc_final: 0.7389 (m) REVERT: H 191 LYS cc_start: 0.6772 (tttp) cc_final: 0.6383 (ttpt) REVERT: H 206 ARG cc_start: 0.6567 (ttm-80) cc_final: 0.5520 (ttm110) REVERT: H 225 ASN cc_start: 0.7533 (m-40) cc_final: 0.6831 (t0) REVERT: H 234 SER cc_start: 0.6888 (m) cc_final: 0.6597 (t) REVERT: H 306 TYR cc_start: 0.8816 (m-80) cc_final: 0.8449 (m-80) REVERT: H 328 LYS cc_start: 0.7139 (mppt) cc_final: 0.6857 (mtpt) REVERT: I 50 LYS cc_start: 0.7278 (mmpt) cc_final: 0.6917 (mtpt) REVERT: I 68 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7472 (mttt) REVERT: I 95 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6927 (mtt-85) REVERT: I 215 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7254 (mttp) REVERT: I 305 MET cc_start: 0.8333 (mmm) cc_final: 0.7836 (mmm) REVERT: M 78 ASN cc_start: 0.7485 (t0) cc_final: 0.7233 (t160) REVERT: M 194 THR cc_start: 0.8087 (m) cc_final: 0.7824 (p) REVERT: M 202 THR cc_start: 0.7919 (m) cc_final: 0.7688 (p) REVERT: M 206 ARG cc_start: 0.7777 (ttp80) cc_final: 0.6951 (ttm110) REVERT: M 224 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7299 (pm20) REVERT: N 47 MET cc_start: 0.1109 (ttp) cc_final: 0.0420 (ttm) REVERT: N 206 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6639 (ttm110) REVERT: N 211 ASP cc_start: 0.7606 (m-30) cc_final: 0.7340 (t70) REVERT: N 305 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7768 (mmt) REVERT: N 328 LYS cc_start: 0.7500 (tptt) cc_final: 0.7089 (tptm) REVERT: N 355 MET cc_start: 0.7822 (mtp) cc_final: 0.7377 (mtt) REVERT: O 68 LYS cc_start: 0.7979 (ptmt) cc_final: 0.7655 (ptpp) REVERT: O 72 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6510 (mp0) REVERT: O 100 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7512 (mt-10) REVERT: O 206 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.6241 (ttm-80) REVERT: O 248 ILE cc_start: 0.7735 (mp) cc_final: 0.7525 (pp) REVERT: O 276 GLU cc_start: 0.6960 (tt0) cc_final: 0.6711 (tt0) REVERT: O 284 LYS cc_start: 0.7683 (mttm) cc_final: 0.7382 (mtpm) REVERT: O 326 LYS cc_start: 0.7494 (ptpp) cc_final: 0.6618 (mmmt) REVERT: O 328 LYS cc_start: 0.7819 (mtmt) cc_final: 0.6885 (tptm) REVERT: O 359 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7661 (tptp) REVERT: P 68 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7820 (ptpt) REVERT: P 82 MET cc_start: 0.7891 (tpt) cc_final: 0.7367 (tpt) REVERT: P 141 SER cc_start: 0.7968 (t) cc_final: 0.7665 (m) REVERT: P 355 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8014 (mpp) REVERT: P 359 LYS cc_start: 0.7265 (ptmm) cc_final: 0.6837 (tptt) REVERT: Q 6 THR cc_start: 0.7991 (p) cc_final: 0.7463 (t) REVERT: Q 34 ILE cc_start: 0.8409 (mt) cc_final: 0.8140 (pt) REVERT: Q 47 MET cc_start: 0.6609 (mmm) cc_final: 0.5631 (ptt) REVERT: Q 61 LYS cc_start: 0.7398 (mtpp) cc_final: 0.7187 (mttp) REVERT: Q 72 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6697 (mt-10) REVERT: Q 190 MET cc_start: 0.7358 (mtm) cc_final: 0.7052 (mtp) REVERT: Q 286 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6791 (m-30) REVERT: Q 291 LYS cc_start: 0.5340 (mttm) cc_final: 0.4736 (tmtm) REVERT: Q 313 MET cc_start: 0.8016 (tpt) cc_final: 0.7531 (mmm) REVERT: Q 328 LYS cc_start: 0.7382 (ttmt) cc_final: 0.6616 (ttmt) REVERT: Q 336 LYS cc_start: 0.7725 (tptm) cc_final: 0.7460 (ttmt) REVERT: Q 354 GLN cc_start: 0.7787 (pm20) cc_final: 0.7288 (mm110) REVERT: R 72 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7016 (mt-10) REVERT: R 99 GLU cc_start: 0.7297 (pt0) cc_final: 0.7056 (pm20) REVERT: R 206 ARG cc_start: 0.6785 (tpp80) cc_final: 0.6192 (ttm-80) REVERT: R 215 LYS cc_start: 0.7502 (mmmt) cc_final: 0.7204 (mptm) REVERT: R 225 ASN cc_start: 0.6581 (t0) cc_final: 0.6097 (m-40) REVERT: R 358 THR cc_start: 0.7781 (m) cc_final: 0.7481 (p) outliers start: 100 outliers final: 48 residues processed: 659 average time/residue: 2.8294 time to fit residues: 2271.9062 Evaluate side-chains 644 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 575 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 286 ASP Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 291 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 370 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN G 19 GLN G 130 HIS O 225 ASN R 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 39895 Z= 0.318 Angle : 0.611 7.795 54139 Z= 0.306 Chirality : 0.045 0.228 5990 Planarity : 0.005 0.078 6962 Dihedral : 8.742 172.264 5541 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.38 % Allowed : 16.67 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.12), residues: 4854 helix: 0.36 (0.12), residues: 1952 sheet: -0.14 (0.17), residues: 875 loop : 0.63 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 387 HIS 0.008 0.001 HIS I 173 PHE 0.017 0.001 PHE D 10 TYR 0.020 0.001 TYR I 279 ARG 0.011 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 677 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 577 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7299 (pt0) cc_final: 0.6978 (pp20) REVERT: A 137 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5844 (mp0) REVERT: A 207 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6674 (tppt) REVERT: A 239 ARG cc_start: 0.5784 (mtt180) cc_final: 0.5356 (mtm-85) REVERT: A 242 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.5883 (mp0) REVERT: A 253 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6126 (mptt) REVERT: A 302 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6544 (m-30) REVERT: A 340 LYS cc_start: 0.7150 (tptp) cc_final: 0.6695 (ttpt) REVERT: A 356 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6791 (tm-30) REVERT: A 365 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7669 (p) REVERT: A 406 LYS cc_start: 0.6972 (pttp) cc_final: 0.6574 (ptpt) REVERT: B 68 LYS cc_start: 0.6680 (mtmt) cc_final: 0.6228 (mtmt) REVERT: B 73 ASN cc_start: 0.7617 (m-40) cc_final: 0.7124 (t0) REVERT: B 96 ILE cc_start: 0.7820 (mm) cc_final: 0.7497 (pt) REVERT: B 228 LYS cc_start: 0.6677 (ttpt) cc_final: 0.5960 (ttpp) REVERT: B 295 ARG cc_start: 0.6667 (mtp180) cc_final: 0.5557 (mpt-90) REVERT: B 364 ASN cc_start: 0.7286 (m-40) cc_final: 0.6709 (t0) REVERT: C 22 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7298 (mp10) REVERT: C 83 GLU cc_start: 0.7023 (tt0) cc_final: 0.6267 (mp0) REVERT: C 91 LYS cc_start: 0.7494 (ttpt) cc_final: 0.6025 (tptp) REVERT: C 251 GLN cc_start: 0.7488 (mt0) cc_final: 0.7012 (mp10) REVERT: C 359 ASN cc_start: 0.6850 (m110) cc_final: 0.6120 (t0) REVERT: D 13 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6123 (mt-10) REVERT: D 47 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7186 (mttp) REVERT: D 73 GLN cc_start: 0.7083 (tt0) cc_final: 0.6829 (mt0) REVERT: D 84 MET cc_start: 0.7151 (mpp) cc_final: 0.6871 (tmm) REVERT: D 165 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: D 172 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6625 (mt-10) REVERT: D 185 ARG cc_start: 0.7705 (ptp-170) cc_final: 0.7408 (ptp-170) REVERT: D 186 GLU cc_start: 0.6367 (tp30) cc_final: 0.6139 (tp30) REVERT: D 255 ARG cc_start: 0.6011 (mtm110) cc_final: 0.5425 (mtt90) REVERT: D 269 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6456 (mp) REVERT: D 287 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.5382 (mtp180) REVERT: E 58 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7052 (ptm160) REVERT: E 94 ARG cc_start: 0.7562 (mtp180) cc_final: 0.7143 (mtp180) REVERT: E 98 SER cc_start: 0.6867 (t) cc_final: 0.6508 (m) REVERT: F 23 GLU cc_start: 0.7591 (tt0) cc_final: 0.7211 (tt0) REVERT: F 56 ASN cc_start: 0.7239 (m-40) cc_final: 0.6928 (m-40) REVERT: F 58 GLN cc_start: 0.7466 (mp-120) cc_final: 0.6053 (tp-100) REVERT: F 81 GLU cc_start: 0.6911 (mp0) cc_final: 0.5903 (mm-30) REVERT: F 97 ARG cc_start: 0.7308 (mmm160) cc_final: 0.6947 (mmm160) REVERT: F 107 LYS cc_start: 0.7060 (mmmm) cc_final: 0.6745 (mttt) REVERT: F 119 THR cc_start: 0.7345 (m) cc_final: 0.7062 (p) REVERT: F 145 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5302 (mm-30) REVERT: F 148 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6545 (tt0) REVERT: G 98 GLU cc_start: 0.6932 (pp20) cc_final: 0.6708 (pp20) REVERT: G 132 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6437 (mppt) REVERT: G 135 GLU cc_start: 0.6628 (tt0) cc_final: 0.6417 (tt0) REVERT: H 25 ASP cc_start: 0.8271 (p0) cc_final: 0.7475 (m-30) REVERT: H 28 ARG cc_start: 0.7689 (tpp-160) cc_final: 0.7383 (tpp80) REVERT: H 68 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7549 (mttm) REVERT: H 72 GLU cc_start: 0.6785 (tt0) cc_final: 0.6282 (mp0) REVERT: H 141 SER cc_start: 0.7815 (t) cc_final: 0.7428 (m) REVERT: H 187 ASP cc_start: 0.7542 (m-30) cc_final: 0.7323 (m-30) REVERT: H 191 LYS cc_start: 0.6776 (tttp) cc_final: 0.6291 (ttpt) REVERT: H 206 ARG cc_start: 0.6619 (ttm-80) cc_final: 0.6125 (ttt180) REVERT: H 225 ASN cc_start: 0.7541 (m-40) cc_final: 0.6834 (t0) REVERT: H 234 SER cc_start: 0.6854 (m) cc_final: 0.6563 (t) REVERT: H 306 TYR cc_start: 0.8849 (m-80) cc_final: 0.8524 (m-80) REVERT: I 50 LYS cc_start: 0.7282 (mmpt) cc_final: 0.6912 (mtpt) REVERT: I 68 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7485 (mttt) REVERT: I 119 MET cc_start: 0.7367 (ttm) cc_final: 0.7071 (ttm) REVERT: I 180 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7229 (tt) REVERT: I 215 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7252 (mttp) REVERT: I 305 MET cc_start: 0.8359 (mmm) cc_final: 0.7857 (mmm) REVERT: M 194 THR cc_start: 0.8127 (m) cc_final: 0.7863 (p) REVERT: M 202 THR cc_start: 0.7941 (m) cc_final: 0.7727 (p) REVERT: M 206 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7438 (ttm110) REVERT: M 224 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7294 (pm20) REVERT: N 47 MET cc_start: 0.1004 (ttp) cc_final: 0.0308 (ttm) REVERT: N 206 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6651 (ttm110) REVERT: N 211 ASP cc_start: 0.7609 (m-30) cc_final: 0.7338 (t70) REVERT: N 236 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7638 (mp) REVERT: N 305 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7807 (mmt) REVERT: N 328 LYS cc_start: 0.7505 (tptt) cc_final: 0.7086 (tptm) REVERT: O 68 LYS cc_start: 0.8000 (ptmt) cc_final: 0.7438 (mtpp) REVERT: O 72 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: O 100 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7577 (mt-10) REVERT: O 206 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.6280 (ttm-80) REVERT: O 248 ILE cc_start: 0.7727 (mp) cc_final: 0.7514 (pp) REVERT: O 276 GLU cc_start: 0.7004 (tt0) cc_final: 0.6787 (tt0) REVERT: O 284 LYS cc_start: 0.7733 (mttm) cc_final: 0.7390 (mtpm) REVERT: O 326 LYS cc_start: 0.7592 (ptpp) cc_final: 0.6776 (mmmt) REVERT: O 328 LYS cc_start: 0.7797 (mtmt) cc_final: 0.6823 (tptm) REVERT: O 359 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7652 (tptp) REVERT: P 68 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7818 (ptpt) REVERT: P 82 MET cc_start: 0.7905 (tpt) cc_final: 0.7323 (tpt) REVERT: P 141 SER cc_start: 0.8000 (t) cc_final: 0.7671 (m) REVERT: P 206 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6321 (ttm110) REVERT: P 241 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: P 355 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7999 (mpp) REVERT: P 359 LYS cc_start: 0.7294 (ptmm) cc_final: 0.6871 (tptt) REVERT: Q 6 THR cc_start: 0.7994 (p) cc_final: 0.7433 (t) REVERT: Q 34 ILE cc_start: 0.8429 (mt) cc_final: 0.8134 (pt) REVERT: Q 47 MET cc_start: 0.6702 (mmm) cc_final: 0.5646 (ptt) REVERT: Q 61 LYS cc_start: 0.7520 (mtpp) cc_final: 0.7296 (mttp) REVERT: Q 72 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6693 (mt-10) REVERT: Q 190 MET cc_start: 0.7437 (mtm) cc_final: 0.7129 (mtp) REVERT: Q 225 ASN cc_start: 0.7071 (t0) cc_final: 0.6591 (m110) REVERT: Q 286 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: Q 291 LYS cc_start: 0.5385 (mttm) cc_final: 0.4774 (tmtm) REVERT: Q 313 MET cc_start: 0.8067 (tpt) cc_final: 0.7580 (mmm) REVERT: Q 328 LYS cc_start: 0.7370 (ttmt) cc_final: 0.6602 (ttmt) REVERT: Q 336 LYS cc_start: 0.7749 (tptm) cc_final: 0.7468 (ttmt) REVERT: Q 354 GLN cc_start: 0.7787 (pm20) cc_final: 0.7282 (mm110) REVERT: R 72 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7026 (mt-10) REVERT: R 99 GLU cc_start: 0.7291 (pt0) cc_final: 0.7023 (pm20) REVERT: R 106 THR cc_start: 0.8553 (m) cc_final: 0.8288 (p) REVERT: R 107 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6205 (tp30) REVERT: R 206 ARG cc_start: 0.6838 (tpp80) cc_final: 0.6200 (ttm-80) REVERT: R 215 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7248 (mptm) REVERT: R 225 ASN cc_start: 0.6602 (t0) cc_final: 0.6101 (m-40) REVERT: R 358 THR cc_start: 0.7787 (m) cc_final: 0.7496 (p) outliers start: 100 outliers final: 54 residues processed: 641 average time/residue: 2.9695 time to fit residues: 2333.9163 Evaluate side-chains 648 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 567 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 241 GLU Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 286 ASP Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 428 optimal weight: 2.9990 chunk 451 optimal weight: 2.9990 chunk 411 optimal weight: 3.9990 chunk 439 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 344 optimal weight: 0.8980 chunk 134 optimal weight: 0.2980 chunk 396 optimal weight: 0.9990 chunk 415 optimal weight: 3.9990 chunk 437 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN O 225 ASN R 137 GLN R 297 ASN R 353 GLN R 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39895 Z= 0.182 Angle : 0.567 6.941 54139 Z= 0.281 Chirality : 0.043 0.198 5990 Planarity : 0.004 0.088 6962 Dihedral : 8.453 172.056 5541 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.79 % Allowed : 17.41 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 4854 helix: 0.54 (0.12), residues: 1953 sheet: -0.20 (0.17), residues: 887 loop : 0.72 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 102 HIS 0.008 0.001 HIS I 173 PHE 0.015 0.001 PHE D 10 TYR 0.015 0.001 TYR I 279 ARG 0.011 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 660 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 585 time to evaluate : 4.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7282 (pt0) cc_final: 0.7010 (pp20) REVERT: A 207 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6633 (tppt) REVERT: A 239 ARG cc_start: 0.5790 (mtt180) cc_final: 0.5296 (mtm-85) REVERT: A 253 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.6097 (mptt) REVERT: A 302 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: A 340 LYS cc_start: 0.7156 (tptp) cc_final: 0.6688 (ttpt) REVERT: A 356 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6798 (tm-30) REVERT: A 365 SER cc_start: 0.8443 (t) cc_final: 0.7750 (p) REVERT: A 406 LYS cc_start: 0.6900 (pttp) cc_final: 0.6482 (ptpt) REVERT: B 68 LYS cc_start: 0.6695 (mtmt) cc_final: 0.6212 (mtmm) REVERT: B 73 ASN cc_start: 0.7603 (m-40) cc_final: 0.7123 (t0) REVERT: B 96 ILE cc_start: 0.7811 (mm) cc_final: 0.7510 (pt) REVERT: B 228 LYS cc_start: 0.6658 (ttpt) cc_final: 0.5939 (ttpp) REVERT: B 295 ARG cc_start: 0.6644 (mtp180) cc_final: 0.5543 (mpt-90) REVERT: B 300 SER cc_start: 0.7653 (t) cc_final: 0.7288 (p) REVERT: B 364 ASN cc_start: 0.7251 (m-40) cc_final: 0.6668 (t0) REVERT: C 22 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7290 (mp10) REVERT: C 83 GLU cc_start: 0.6983 (tt0) cc_final: 0.6250 (mp0) REVERT: C 91 LYS cc_start: 0.7512 (ttpt) cc_final: 0.6041 (tptp) REVERT: C 251 GLN cc_start: 0.7469 (mt0) cc_final: 0.7008 (mp10) REVERT: C 359 ASN cc_start: 0.6806 (m110) cc_final: 0.6037 (t0) REVERT: D 13 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6103 (mt-10) REVERT: D 47 LYS cc_start: 0.7640 (mtmm) cc_final: 0.7100 (mttp) REVERT: D 73 GLN cc_start: 0.7102 (tt0) cc_final: 0.6793 (mt0) REVERT: D 84 MET cc_start: 0.7166 (mpp) cc_final: 0.6882 (tmm) REVERT: D 143 ASN cc_start: 0.6785 (m-40) cc_final: 0.6518 (t0) REVERT: D 172 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6606 (mt-10) REVERT: D 185 ARG cc_start: 0.7690 (ptp-170) cc_final: 0.7411 (ptp-170) REVERT: D 186 GLU cc_start: 0.6334 (tp30) cc_final: 0.5844 (mm-30) REVERT: D 255 ARG cc_start: 0.6022 (mtm110) cc_final: 0.5418 (mtt90) REVERT: D 287 ARG cc_start: 0.5959 (OUTLIER) cc_final: 0.5257 (mtp180) REVERT: E 58 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7045 (ptm160) REVERT: E 94 ARG cc_start: 0.7556 (mtp180) cc_final: 0.7131 (mtp180) REVERT: E 98 SER cc_start: 0.6895 (t) cc_final: 0.6540 (m) REVERT: F 23 GLU cc_start: 0.7586 (tt0) cc_final: 0.7216 (tt0) REVERT: F 56 ASN cc_start: 0.7135 (m-40) cc_final: 0.6730 (m-40) REVERT: F 58 GLN cc_start: 0.7404 (mp-120) cc_final: 0.5964 (tp-100) REVERT: F 81 GLU cc_start: 0.6918 (mp0) cc_final: 0.5867 (mm-30) REVERT: F 97 ARG cc_start: 0.7308 (mmm160) cc_final: 0.6956 (mmm160) REVERT: F 107 LYS cc_start: 0.7045 (mmmm) cc_final: 0.6673 (mttt) REVERT: F 119 THR cc_start: 0.7291 (m) cc_final: 0.7009 (p) REVERT: F 145 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5299 (mm-30) REVERT: G 98 GLU cc_start: 0.6976 (pp20) cc_final: 0.6757 (pp20) REVERT: G 132 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6423 (mppt) REVERT: H 25 ASP cc_start: 0.8240 (p0) cc_final: 0.7475 (m-30) REVERT: H 28 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7395 (tpp80) REVERT: H 30 VAL cc_start: 0.8704 (m) cc_final: 0.8417 (t) REVERT: H 68 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7462 (mttm) REVERT: H 72 GLU cc_start: 0.6768 (tt0) cc_final: 0.6257 (mp0) REVERT: H 141 SER cc_start: 0.7761 (t) cc_final: 0.7386 (m) REVERT: H 206 ARG cc_start: 0.6548 (ttm-80) cc_final: 0.5502 (ttm110) REVERT: H 225 ASN cc_start: 0.7536 (m-40) cc_final: 0.6799 (t0) REVERT: H 234 SER cc_start: 0.6769 (m) cc_final: 0.6494 (t) REVERT: H 306 TYR cc_start: 0.8821 (m-80) cc_final: 0.8500 (m-80) REVERT: I 50 LYS cc_start: 0.7223 (mmpt) cc_final: 0.6863 (mtpt) REVERT: I 68 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7494 (mttt) REVERT: I 119 MET cc_start: 0.7354 (ttm) cc_final: 0.7044 (ttm) REVERT: I 215 LYS cc_start: 0.7682 (mtpp) cc_final: 0.7258 (mttp) REVERT: I 305 MET cc_start: 0.8341 (mmm) cc_final: 0.7853 (mmm) REVERT: M 78 ASN cc_start: 0.7425 (t0) cc_final: 0.7166 (t160) REVERT: M 194 THR cc_start: 0.8086 (m) cc_final: 0.7845 (p) REVERT: M 202 THR cc_start: 0.7904 (m) cc_final: 0.7704 (p) REVERT: M 206 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7488 (ttm110) REVERT: M 224 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7299 (pm20) REVERT: M 355 MET cc_start: 0.7526 (mtp) cc_final: 0.7227 (mtp) REVERT: N 47 MET cc_start: 0.1035 (ttp) cc_final: 0.0363 (ttm) REVERT: N 211 ASP cc_start: 0.7600 (m-30) cc_final: 0.7249 (t70) REVERT: N 305 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7695 (mmt) REVERT: N 328 LYS cc_start: 0.7519 (tptt) cc_final: 0.7104 (tptm) REVERT: O 68 LYS cc_start: 0.7941 (ptmt) cc_final: 0.7394 (mtpp) REVERT: O 72 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: O 82 MET cc_start: 0.8246 (tpt) cc_final: 0.7808 (tpt) REVERT: O 100 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7491 (mt-10) REVERT: O 206 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.6242 (ttm-80) REVERT: O 276 GLU cc_start: 0.6947 (tt0) cc_final: 0.6739 (tt0) REVERT: O 284 LYS cc_start: 0.7672 (mttm) cc_final: 0.7366 (mtpm) REVERT: O 326 LYS cc_start: 0.7497 (ptpp) cc_final: 0.6594 (mmmt) REVERT: O 328 LYS cc_start: 0.7787 (mtmt) cc_final: 0.6829 (tptm) REVERT: O 359 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7681 (tptp) REVERT: P 68 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7751 (ptpt) REVERT: P 82 MET cc_start: 0.7874 (tpt) cc_final: 0.7364 (tpt) REVERT: P 141 SER cc_start: 0.7966 (t) cc_final: 0.7692 (m) REVERT: P 355 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8008 (mpp) REVERT: P 359 LYS cc_start: 0.7263 (ptmm) cc_final: 0.6843 (tptt) REVERT: Q 6 THR cc_start: 0.7975 (p) cc_final: 0.7426 (t) REVERT: Q 34 ILE cc_start: 0.8417 (mt) cc_final: 0.8143 (pt) REVERT: Q 47 MET cc_start: 0.6661 (mmm) cc_final: 0.5655 (ptt) REVERT: Q 72 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: Q 190 MET cc_start: 0.7357 (mtm) cc_final: 0.7055 (mtp) REVERT: Q 291 LYS cc_start: 0.5338 (mttm) cc_final: 0.4769 (tmtm) REVERT: Q 313 MET cc_start: 0.8006 (tpt) cc_final: 0.7645 (mmm) REVERT: Q 328 LYS cc_start: 0.7354 (ttmt) cc_final: 0.6576 (ttmt) REVERT: Q 336 LYS cc_start: 0.7746 (tptm) cc_final: 0.7465 (ttmt) REVERT: Q 354 GLN cc_start: 0.7765 (pm20) cc_final: 0.7268 (mm110) REVERT: R 47 MET cc_start: 0.5860 (ppp) cc_final: 0.5403 (ppp) REVERT: R 72 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7032 (mt-10) REVERT: R 99 GLU cc_start: 0.7331 (pt0) cc_final: 0.7090 (pm20) REVERT: R 106 THR cc_start: 0.8428 (m) cc_final: 0.8144 (p) REVERT: R 206 ARG cc_start: 0.6761 (tpp80) cc_final: 0.6170 (ttm-80) REVERT: R 215 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7221 (mptm) REVERT: R 225 ASN cc_start: 0.6584 (t0) cc_final: 0.6082 (m-40) REVERT: R 358 THR cc_start: 0.7761 (m) cc_final: 0.7491 (p) outliers start: 75 outliers final: 46 residues processed: 630 average time/residue: 2.8301 time to fit residues: 2165.2352 Evaluate side-chains 636 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 576 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain O residue 12 ASN Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 288 optimal weight: 5.9990 chunk 464 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 487 optimal weight: 2.9990 chunk 448 optimal weight: 1.9990 chunk 387 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 299 optimal weight: 0.6980 chunk 237 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN O 225 ASN P 297 ASN Q 137 GLN R 297 ASN R 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39895 Z= 0.210 Angle : 0.573 7.783 54139 Z= 0.284 Chirality : 0.043 0.203 5990 Planarity : 0.004 0.091 6962 Dihedral : 8.334 172.335 5540 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.57 % Allowed : 17.75 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.12), residues: 4854 helix: 0.60 (0.12), residues: 1958 sheet: -0.18 (0.17), residues: 887 loop : 0.74 (0.15), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 102 HIS 0.008 0.001 HIS I 173 PHE 0.014 0.001 PHE B 351 TYR 0.015 0.001 TYR I 279 ARG 0.013 0.000 ARG F 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 641 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 575 time to evaluate : 4.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7340 (pt0) cc_final: 0.7069 (pp20) REVERT: A 207 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6641 (tppt) REVERT: A 239 ARG cc_start: 0.5781 (mtt180) cc_final: 0.5263 (mtm-85) REVERT: A 242 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.5944 (mp0) REVERT: A 253 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6103 (mptt) REVERT: A 302 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: A 340 LYS cc_start: 0.7146 (tptp) cc_final: 0.6678 (ttpt) REVERT: A 356 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6801 (tm-30) REVERT: A 365 SER cc_start: 0.8449 (t) cc_final: 0.7784 (p) REVERT: A 406 LYS cc_start: 0.6935 (pttp) cc_final: 0.6498 (ptpt) REVERT: B 68 LYS cc_start: 0.6690 (mtmt) cc_final: 0.6285 (mtmt) REVERT: B 73 ASN cc_start: 0.7621 (m-40) cc_final: 0.7157 (t0) REVERT: B 96 ILE cc_start: 0.7761 (mm) cc_final: 0.7490 (pt) REVERT: B 224 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6566 (mm-30) REVERT: B 228 LYS cc_start: 0.6668 (ttpt) cc_final: 0.5949 (ttpp) REVERT: B 295 ARG cc_start: 0.6654 (mtp180) cc_final: 0.5573 (mpt-90) REVERT: B 300 SER cc_start: 0.7696 (t) cc_final: 0.7314 (p) REVERT: B 364 ASN cc_start: 0.7253 (m-40) cc_final: 0.6540 (t0) REVERT: C 22 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7299 (mp10) REVERT: C 39 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6911 (pt0) REVERT: C 41 ASP cc_start: 0.6157 (t0) cc_final: 0.5163 (p0) REVERT: C 83 GLU cc_start: 0.6995 (tt0) cc_final: 0.6249 (mp0) REVERT: C 251 GLN cc_start: 0.7471 (mt0) cc_final: 0.7013 (mp10) REVERT: C 359 ASN cc_start: 0.6817 (m110) cc_final: 0.6063 (t0) REVERT: D 13 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6068 (mt-10) REVERT: D 17 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6569 (tm-30) REVERT: D 47 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7078 (mttp) REVERT: D 73 GLN cc_start: 0.7075 (tt0) cc_final: 0.6768 (mt0) REVERT: D 84 MET cc_start: 0.7144 (mpp) cc_final: 0.6870 (tmm) REVERT: D 102 GLU cc_start: 0.6351 (mp0) cc_final: 0.6064 (mp0) REVERT: D 143 ASN cc_start: 0.6818 (m-40) cc_final: 0.6527 (t0) REVERT: D 172 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6633 (mt-10) REVERT: D 185 ARG cc_start: 0.7680 (ptp-170) cc_final: 0.7394 (ptp-170) REVERT: D 186 GLU cc_start: 0.6308 (tp30) cc_final: 0.5836 (mm-30) REVERT: D 255 ARG cc_start: 0.6038 (mtm110) cc_final: 0.5424 (mtt90) REVERT: D 287 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.5252 (mtp180) REVERT: E 58 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7021 (ptm160) REVERT: E 94 ARG cc_start: 0.7550 (mtp180) cc_final: 0.7128 (mtp180) REVERT: E 98 SER cc_start: 0.6917 (t) cc_final: 0.6560 (m) REVERT: F 23 GLU cc_start: 0.7586 (tt0) cc_final: 0.7211 (tt0) REVERT: F 56 ASN cc_start: 0.7161 (m-40) cc_final: 0.6765 (m-40) REVERT: F 58 GLN cc_start: 0.7390 (mp-120) cc_final: 0.5965 (tp-100) REVERT: F 81 GLU cc_start: 0.6884 (mp0) cc_final: 0.5824 (mm-30) REVERT: F 97 ARG cc_start: 0.7326 (mmm160) cc_final: 0.6971 (mmm160) REVERT: F 107 LYS cc_start: 0.7050 (mmmm) cc_final: 0.6679 (mttt) REVERT: F 119 THR cc_start: 0.7320 (m) cc_final: 0.7034 (p) REVERT: F 145 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5224 (mm-30) REVERT: G 103 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6981 (mt-10) REVERT: G 132 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6424 (mppt) REVERT: H 25 ASP cc_start: 0.8241 (p0) cc_final: 0.7472 (m-30) REVERT: H 28 ARG cc_start: 0.7705 (tpp-160) cc_final: 0.7400 (tpp80) REVERT: H 30 VAL cc_start: 0.8708 (m) cc_final: 0.8433 (t) REVERT: H 68 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7471 (mttm) REVERT: H 72 GLU cc_start: 0.6766 (tt0) cc_final: 0.6251 (mp0) REVERT: H 141 SER cc_start: 0.7761 (t) cc_final: 0.7384 (m) REVERT: H 165 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7183 (mt) REVERT: H 187 ASP cc_start: 0.7443 (m-30) cc_final: 0.7148 (m-30) REVERT: H 206 ARG cc_start: 0.6521 (ttm-80) cc_final: 0.5442 (ttm110) REVERT: H 225 ASN cc_start: 0.7540 (m-40) cc_final: 0.6795 (t0) REVERT: H 234 SER cc_start: 0.6779 (m) cc_final: 0.6513 (t) REVERT: H 306 TYR cc_start: 0.8823 (m-80) cc_final: 0.8503 (m-80) REVERT: I 50 LYS cc_start: 0.7197 (mmpt) cc_final: 0.6834 (mtpt) REVERT: I 68 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7505 (mttt) REVERT: I 119 MET cc_start: 0.7315 (ttm) cc_final: 0.7056 (ttm) REVERT: I 215 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7257 (mttp) REVERT: I 305 MET cc_start: 0.8344 (mmm) cc_final: 0.7859 (mmm) REVERT: M 78 ASN cc_start: 0.7428 (t0) cc_final: 0.7182 (t160) REVERT: M 194 THR cc_start: 0.8088 (m) cc_final: 0.7859 (p) REVERT: M 202 THR cc_start: 0.7911 (m) cc_final: 0.7710 (p) REVERT: M 206 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7484 (ttm110) REVERT: M 224 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7309 (pm20) REVERT: M 355 MET cc_start: 0.7552 (mtp) cc_final: 0.7251 (mtp) REVERT: N 47 MET cc_start: 0.0973 (ttp) cc_final: 0.0313 (ttm) REVERT: N 211 ASP cc_start: 0.7603 (m-30) cc_final: 0.7250 (t70) REVERT: N 305 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7725 (mmt) REVERT: N 328 LYS cc_start: 0.7504 (tptt) cc_final: 0.7098 (tptm) REVERT: O 68 LYS cc_start: 0.7938 (ptmt) cc_final: 0.7398 (mtpp) REVERT: O 72 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: O 82 MET cc_start: 0.8262 (tpt) cc_final: 0.7831 (tpt) REVERT: O 100 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7492 (mt-10) REVERT: O 206 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.6253 (ttm-80) REVERT: O 284 LYS cc_start: 0.7684 (mttm) cc_final: 0.7374 (mtpm) REVERT: O 326 LYS cc_start: 0.7515 (ptpp) cc_final: 0.6703 (mmmt) REVERT: O 328 LYS cc_start: 0.7792 (mtmt) cc_final: 0.6828 (tptm) REVERT: O 359 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7672 (tptp) REVERT: P 82 MET cc_start: 0.7880 (tpt) cc_final: 0.7368 (tpt) REVERT: P 141 SER cc_start: 0.7990 (t) cc_final: 0.7712 (m) REVERT: P 206 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6291 (ttm110) REVERT: P 355 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8018 (mpp) REVERT: P 359 LYS cc_start: 0.7245 (ptmm) cc_final: 0.6845 (tptt) REVERT: Q 6 THR cc_start: 0.7969 (p) cc_final: 0.7418 (t) REVERT: Q 34 ILE cc_start: 0.8427 (mt) cc_final: 0.8155 (pt) REVERT: Q 47 MET cc_start: 0.6700 (mmm) cc_final: 0.5674 (ptt) REVERT: Q 72 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: Q 190 MET cc_start: 0.7360 (mtm) cc_final: 0.7143 (mtp) REVERT: Q 291 LYS cc_start: 0.5328 (mttm) cc_final: 0.4777 (tmtm) REVERT: Q 313 MET cc_start: 0.8007 (tpt) cc_final: 0.7512 (mmm) REVERT: Q 328 LYS cc_start: 0.7353 (ttmt) cc_final: 0.6572 (ttmt) REVERT: Q 336 LYS cc_start: 0.7744 (tptm) cc_final: 0.7471 (ttmt) REVERT: Q 354 GLN cc_start: 0.7755 (pm20) cc_final: 0.7270 (mm110) REVERT: R 47 MET cc_start: 0.5891 (ppp) cc_final: 0.5399 (ppp) REVERT: R 72 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7035 (mt-10) REVERT: R 99 GLU cc_start: 0.7316 (pt0) cc_final: 0.7094 (pm20) REVERT: R 106 THR cc_start: 0.8335 (m) cc_final: 0.8103 (p) REVERT: R 206 ARG cc_start: 0.6773 (tpp80) cc_final: 0.6173 (ttm-80) REVERT: R 215 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7224 (mptm) REVERT: R 225 ASN cc_start: 0.6591 (t0) cc_final: 0.6085 (m-40) REVERT: R 358 THR cc_start: 0.7765 (m) cc_final: 0.7503 (p) outliers start: 66 outliers final: 45 residues processed: 612 average time/residue: 2.8700 time to fit residues: 2134.5682 Evaluate side-chains 630 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 569 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 308 optimal weight: 1.9990 chunk 413 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 357 optimal weight: 2.9990 chunk 57 optimal weight: 0.0010 chunk 107 optimal weight: 10.0000 chunk 388 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 398 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN O 225 ASN R 297 ASN R 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114702 restraints weight = 135335.521| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.57 r_work: 0.3294 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39895 Z= 0.169 Angle : 0.556 8.326 54139 Z= 0.274 Chirality : 0.043 0.182 5990 Planarity : 0.004 0.095 6962 Dihedral : 8.059 176.521 5540 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.31 % Allowed : 18.08 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.12), residues: 4854 helix: 0.76 (0.12), residues: 1959 sheet: -0.16 (0.17), residues: 886 loop : 0.82 (0.15), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 102 HIS 0.009 0.001 HIS I 173 PHE 0.012 0.001 PHE I 255 TYR 0.014 0.001 TYR F 8 ARG 0.012 0.000 ARG F 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33613.90 seconds wall clock time: 567 minutes 38.40 seconds (34058.40 seconds total)