Starting phenix.real_space_refine on Sat Jan 25 23:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uxx_42788/01_2025/8uxx_42788_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uxx_42788/01_2025/8uxx_42788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uxx_42788/01_2025/8uxx_42788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uxx_42788/01_2025/8uxx_42788.map" model { file = "/net/cci-nas-00/data/ceres_data/8uxx_42788/01_2025/8uxx_42788_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uxx_42788/01_2025/8uxx_42788_trim.cif" } resolution = 3.2 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= 0.005 sd= 0.077 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: 9 Type Number sf(0) Gaussians P 21 5.49 5 Mg 10 5.21 5 S 230 5.16 5 Be 7 3.05 5 C 24684 2.51 5 N 6643 2.21 5 O 7446 1.98 5 F 21 1.80 5 H 38340 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 281 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 77402 Number of models: 1 Model: "" Number of chains: 26 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 15 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 26.92, per 1000 atoms: 0.35 Number of scatterers: 77402 At special positions: 0 Unit cell: (133.254, 204.592, 228.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 230 16.00 P 21 15.00 Mg 10 11.99 F 21 9.00 O 7446 8.00 N 6643 7.00 C 24684 6.00 Be 7 4.00 H 38340 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=2.08 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.95 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: 258 helices and 73 sheets defined 48.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.78 Creating SS restraints... Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.564A pdb=" N LEU A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 82' 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: 3.696A pdb=" N ARG A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.586A pdb=" N LEU A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' 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: 3.811A pdb=" N GLU A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.819A 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 293 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 removed outlier: 3.608A pdb=" N ASN A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 341 through 366 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 403 removed outlier: 3.687A pdb=" N TYR A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 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: 3.676A pdb=" N GLN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.885A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.506A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.698A pdb=" N ARG B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.227A pdb=" N THR B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.536A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.670A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 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 removed outlier: 3.698A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 323 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.050A 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: 3.702A pdb=" N ASP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 378 removed outlier: 3.933A pdb=" N GLU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.651A 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: 3.558A pdb=" N SER D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.723A pdb=" N ASN D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.760A pdb=" N LEU D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) 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 removed outlier: 3.558A pdb=" N ASP D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 155 removed outlier: 3.714A pdb=" N SER D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 removed outlier: 4.003A pdb=" N VAL D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 removed outlier: 7.145A pdb=" N ALA D 208 " --> pdb=" O ARG D 205 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 210 " --> pdb=" O PRO D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.808A pdb=" N ARG D 227 " --> pdb=" O LEU D 224 " (cutoff:3.500A) 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: 3.886A pdb=" N VAL D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 297 removed outlier: 3.659A pdb=" N GLN D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 removed outlier: 3.613A pdb=" N LEU E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 55 removed outlier: 4.516A pdb=" N ARG E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 84 removed outlier: 3.722A pdb=" N SER E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 102 removed outlier: 4.378A pdb=" N ARG E 94 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 150 removed outlier: 4.122A pdb=" N GLU E 128 " --> pdb=" O PRO E 124 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) removed outlier: 3.677A 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 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 removed outlier: 3.571A pdb=" N GLN F 92 " --> pdb=" O ARG F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 166 removed outlier: 4.824A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.607A 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: 3.686A 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: 3.598A pdb=" N ILE G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 49 removed outlier: 3.691A pdb=" N LEU G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 51 through 60 Processing helix chain 'G' and resid 69 through 85 removed outlier: 4.393A pdb=" N GLN G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 100 through 115 removed outlier: 3.817A pdb=" N ASN G 109 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG G 113 " --> pdb=" O ASN G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 138 removed outlier: 3.946A pdb=" N LEU G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 148 removed outlier: 3.505A pdb=" N VAL G 143 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL G 145 " --> pdb=" O CYS G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 62 Processing helix chain 'H' and resid 78 through 92 removed outlier: 4.393A 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: 3.768A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.816A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 202 through 217 removed outlier: 3.995A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS H 217 " --> pdb=" O LYS H 213 " (cutoff:3.500A) 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 260 removed outlier: 3.544A pdb=" N CYS H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 261 through 262 No H-bonds generated for 'chain 'H' and resid 261 through 262' Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 283 Processing helix chain 'H' and resid 286 through 294 removed outlier: 3.855A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR H 294 " --> pdb=" O ARG H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.364A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.669A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (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 removed outlier: 3.508A pdb=" N SER H 348 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 353 removed outlier: 3.554A pdb=" N GLN H 353 " --> pdb=" O SER H 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 350 through 353' Processing helix chain 'H' and resid 359 through 364 removed outlier: 3.746A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 368 No H-bonds generated for 'chain 'H' and resid 366 through 368' 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: 4.277A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS I 87 " --> pdb=" O GLU I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 112 through 126 removed outlier: 4.079A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU I 117 " --> pdb=" O LYS I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 141 Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.698A 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: 3.840A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 233 removed outlier: 3.851A pdb=" N ALA I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 237 Processing helix chain 'I' and resid 252 through 263 Proline residue: I 258 - end of helix removed outlier: 4.736A pdb=" N LEU I 261 " --> pdb=" O CYS I 257 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE I 262 " --> pdb=" O PRO I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 268 Processing helix chain 'I' and resid 273 through 283 removed outlier: 3.547A pdb=" N THR I 278 " --> pdb=" O ILE I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 294 removed outlier: 4.393A pdb=" N TYR I 294 " --> pdb=" O ARG I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 removed outlier: 3.930A 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 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 337 through 349 Processing helix chain 'I' and resid 351 through 355 removed outlier: 4.037A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 removed outlier: 4.839A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 374 removed outlier: 3.843A pdb=" N LYS I 373 " --> pdb=" O ILE I 369 " (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: 3.857A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 removed outlier: 3.771A pdb=" N SER M 141 " --> pdb=" O GLN M 137 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 193 Processing helix chain 'M' and resid 194 through 197 Processing helix chain 'M' and resid 204 through 214 Processing helix chain 'M' and resid 222 through 231 Processing helix chain 'M' and resid 252 through 257 Processing helix chain 'M' and resid 258 through 262 Processing helix chain 'M' and resid 263 through 268 Processing helix chain 'M' and resid 273 through 285 removed outlier: 3.571A pdb=" N CYS M 285 " --> pdb=" O SER M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 289 through 295 removed outlier: 3.685A pdb=" N ALA M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 306 removed outlier: 4.295A 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 351 through 355 removed outlier: 4.156A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 363 Processing helix chain 'M' and resid 365 through 368 removed outlier: 3.803A pdb=" N SER M 368 " --> pdb=" O ALA M 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 365 through 368' Processing helix chain 'M' and resid 369 through 374 Processing helix chain 'N' and resid 55 through 62 Processing helix chain 'N' and resid 78 through 92 removed outlier: 3.817A pdb=" N LYS N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 101 Processing helix chain 'N' and resid 112 through 126 removed outlier: 4.026A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 145 removed outlier: 3.949A pdb=" N SER N 141 " --> pdb=" O GLN N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 194 removed outlier: 3.819A 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: 4.205A pdb=" N LYS N 215 " --> pdb=" O ASP N 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 231 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 296 Processing helix chain 'N' and resid 301 through 306 removed outlier: 4.430A pdb=" N TYR N 306 " --> pdb=" O THR N 303 " (cutoff:3.500A) 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: 3.783A pdb=" N GLU N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 375 removed outlier: 3.901A pdb=" N ARG N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 3.741A pdb=" N LYS O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 92 removed outlier: 3.886A pdb=" N LYS O 84 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 101 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.893A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET O 123 " --> pdb=" O MET O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 144 removed outlier: 3.998A pdb=" N LEU O 142 " --> pdb=" O ALA O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 175 Processing helix chain 'O' and resid 181 through 194 Processing helix chain 'O' and resid 204 through 217 removed outlier: 4.153A pdb=" N LYS O 215 " --> pdb=" O ASP O 211 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS O 217 " --> pdb=" O LYS O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 231 removed outlier: 3.710A pdb=" N ALA O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) 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 283 Processing helix chain 'O' and resid 284 through 285 No H-bonds generated for 'chain 'O' and resid 284 through 285' Processing helix chain 'O' and resid 286 through 288 No H-bonds generated for 'chain 'O' and resid 286 through 288' Processing helix chain 'O' and resid 289 through 295 Processing helix chain 'O' and resid 301 through 306 removed outlier: 4.321A pdb=" N TYR O 306 " --> pdb=" O THR O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 321 Processing helix chain 'O' and resid 332 through 336 removed outlier: 4.279A pdb=" N LYS O 336 " --> pdb=" O PRO O 333 " (cutoff:3.500A) 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 removed outlier: 3.660A pdb=" N VAL O 370 " --> pdb=" O PRO O 367 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS O 373 " --> pdb=" O VAL O 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 61 Processing helix chain 'P' and resid 78 through 92 removed outlier: 3.702A pdb=" N LYS P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 101 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.760A pdb=" N ARG P 116 " --> pdb=" O PRO P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 146 removed outlier: 4.313A pdb=" N LEU P 142 " --> pdb=" O ALA P 138 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 175 Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.908A pdb=" N GLU P 195 " --> pdb=" O LYS P 191 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG P 196 " --> pdb=" O ILE P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 216 removed outlier: 3.713A pdb=" N GLU P 207 " --> pdb=" O THR P 203 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU P 214 " --> pdb=" O ARG P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 231 Processing helix chain 'P' and resid 252 through 257 removed outlier: 3.766A pdb=" N CYS P 257 " --> pdb=" O GLU P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 262 Processing helix chain 'P' and resid 263 through 268 Processing helix chain 'P' and resid 273 through 283 Processing helix chain 'P' and resid 284 through 285 No H-bonds generated for 'chain 'P' and resid 284 through 285' Processing helix chain 'P' and resid 286 through 288 No H-bonds generated for 'chain 'P' and resid 286 through 288' Processing helix chain 'P' and resid 289 through 295 removed outlier: 3.777A pdb=" N ALA P 295 " --> pdb=" O LYS P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 306 removed outlier: 4.217A pdb=" N TYR P 306 " --> pdb=" O THR P 303 " (cutoff:3.500A) 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 347 Processing helix chain 'P' and resid 359 through 366 Processing helix chain 'P' and resid 367 through 373 removed outlier: 3.708A pdb=" N HIS P 371 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 61 Processing helix chain 'Q' and resid 78 through 92 removed outlier: 3.547A pdb=" N ILE Q 85 " --> pdb=" O ASP Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 101 removed outlier: 3.889A pdb=" N HIS Q 101 " --> pdb=" O PRO Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.865A pdb=" N ARG Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET Q 123 " --> pdb=" O MET Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 146 removed outlier: 3.612A pdb=" N LEU Q 142 " --> pdb=" O ALA Q 138 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR Q 143 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 194 removed outlier: 3.632A pdb=" N THR Q 194 " --> pdb=" O MET Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 197 No H-bonds generated for 'chain 'Q' and resid 195 through 197' Processing helix chain 'Q' and resid 204 through 217 Processing helix chain 'Q' and resid 222 through 231 Processing helix chain 'Q' and resid 252 through 257 removed outlier: 3.550A 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: 3.549A pdb=" N ARG Q 290 " --> pdb=" O ASP Q 286 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 306 removed outlier: 4.310A pdb=" N TYR Q 306 " --> pdb=" O THR Q 303 " (cutoff:3.500A) 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 347 Processing helix chain 'Q' and resid 359 through 364 removed outlier: 3.864A pdb=" N GLU Q 364 " --> pdb=" O GLN Q 360 " (cutoff:3.500A) Processing helix chain 'Q' and resid 366 through 373 removed outlier: 3.814A pdb=" N HIS Q 371 " --> pdb=" O SER Q 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 61 Processing helix chain 'R' and resid 78 through 92 removed outlier: 3.965A pdb=" N LYS R 84 " --> pdb=" O ASP R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.707A pdb=" N ARG R 116 " --> pdb=" O PRO R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.085A pdb=" N SER R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 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: 3.704A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE R 208 " --> pdb=" O ALA R 204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS R 217 " --> pdb=" O LYS R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 230 Processing helix chain 'R' and resid 231 through 236 removed outlier: 7.117A pdb=" N SER R 234 " --> pdb=" O ALA R 231 " (cutoff:3.500A) removed outlier: 3.851A 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: 3.774A pdb=" N CYS R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 295 removed outlier: 3.720A pdb=" N LEU R 293 " --> pdb=" O ILE R 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 306 removed outlier: 4.158A pdb=" N TYR R 306 " --> pdb=" O THR R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 321 removed outlier: 3.524A pdb=" N LEU R 320 " --> pdb=" O GLU R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 336 No H-bonds generated for 'chain 'R' and resid 334 through 336' Processing helix chain 'R' and resid 337 through 347 Processing helix chain 'R' and resid 351 through 355 removed outlier: 4.309A pdb=" N GLN R 354 " --> pdb=" O THR R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 363 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: 6.536A pdb=" N ILE A 8 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 129 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N MET A 10 " --> pdb=" O THR A 129 " (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: 6.667A pdb=" N ILE A 330 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.851A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN B 10 " --> 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 176 through 178 removed outlier: 6.764A pdb=" N ILE B 297 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 165 through 166 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: 6.776A 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: 6.507A pdb=" N ALA C 362 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 14 through 19 removed outlier: 4.687A pdb=" N GLU C 16 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 35 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.905A 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: 3.658A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.658A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C 79 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 103 through 108 removed outlier: 3.866A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.535A pdb=" N SER C 151 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ALA C 170 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU C 201 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 172 " --> pdb=" O CYS C 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 208 through 213 removed outlier: 3.652A pdb=" N ALA C 210 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 243 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 254 through 261 removed outlier: 6.554A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLN C 278 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N HIS C 286 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASN C 280 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TRP C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 32 removed outlier: 4.566A pdb=" N SER D 89 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 157 through 159 Processing sheet with id=AC6, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AC7, first strand: chain 'F' and resid 47 through 54 removed outlier: 5.565A pdb=" N LYS F 49 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER F 65 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.772A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'H' and resid 71 through 72 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 169 through 170 removed outlier: 3.515A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL H 298 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AD5, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.816A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'I' and resid 71 through 72 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 169 through 170 removed outlier: 7.885A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AE2, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.732A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AE5, first strand: chain 'M' and resid 169 through 170 Processing sheet with id=AE6, first strand: chain 'M' and resid 169 through 170 Processing sheet with id=AE7, first strand: chain 'M' and resid 238 through 241 Processing sheet with id=AE8, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.922A pdb=" N LEU N 8 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N THR N 106 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N CYS N 10 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AF2, first strand: chain 'N' and resid 169 through 170 Processing sheet with id=AF3, first strand: chain 'N' and resid 169 through 170 removed outlier: 6.260A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU N 153 " --> pdb=" O SER N 300 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN N 297 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 238 through 241 Processing sheet with id=AF5, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.625A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 53 through 54 removed outlier: 3.572A pdb=" N ARG O 37 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AF8, first strand: chain 'O' and resid 176 through 178 removed outlier: 6.585A pdb=" N ASN O 297 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 176 through 178 removed outlier: 4.308A pdb=" N GLN Q 41 " --> pdb=" O ALA O 170 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 238 through 241 Processing sheet with id=AG2, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.796A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N CYS P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 53 through 54 removed outlier: 3.527A pdb=" N ARG P 37 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 71 through 72 Processing sheet with id=AG5, first strand: chain 'P' and resid 169 through 170 Processing sheet with id=AG6, first strand: chain 'P' and resid 169 through 170 removed outlier: 6.024A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU P 153 " --> pdb=" O SER P 300 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 238 through 241 Processing sheet with id=AG8, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.683A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR Q 106 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N CYS Q 10 " --> pdb=" O THR Q 106 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AH1, first strand: chain 'Q' and resid 71 through 72 Processing sheet with id=AH2, first strand: chain 'Q' and resid 169 through 170 Processing sheet with id=AH3, first strand: chain 'Q' and resid 169 through 170 removed outlier: 3.547A pdb=" N VAL Q 163 " --> pdb=" O VAL Q 152 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN Q 297 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id=AH5, first strand: chain 'R' and resid 29 through 32 Processing sheet with id=AH6, first strand: chain 'R' and resid 53 through 54 Processing sheet with id=AH7, first strand: chain 'R' and resid 71 through 72 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 169 through 170 removed outlier: 3.585A pdb=" N VAL R 163 " --> pdb=" O VAL R 152 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN R 297 " --> pdb=" O ILE R 330 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 238 through 241 1849 hydrogen bonds defined for protein. 4782 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: 34.81 Time building geometry restraints manager: 18.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 38277 1.13 - 1.30: 7043 1.30 - 1.48: 15449 1.48 - 1.65: 17092 1.65 - 1.83: 395 Bond restraints: 78256 Sorted by residual: bond pdb=" N HIS H 101 " pdb=" H HIS H 101 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N THR Q 77 " pdb=" H THR Q 77 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N SER M 141 " pdb=" H SER M 141 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 GLN C 131 " pdb="HE22 GLN C 131 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CZ PHE Q 90 " pdb=" HZ PHE Q 90 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 78251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 135120 4.70 - 9.41: 6068 9.41 - 14.11: 96 14.11 - 18.81: 22 18.81 - 23.51: 6 Bond angle restraints: 141312 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 136.83 119.58 17.25 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 123.50 16.37 1.00e+00 1.00e+00 2.68e+02 angle pdb=" F2 BEF Q 403 " pdb="BE BEF Q 403 " pdb=" F3 BEF Q 403 " ideal model delta sigma weight residual 119.96 96.45 23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" O1B ADP H 802 " pdb=" PB ADP H 802 " pdb=" O3B ADP H 802 " ideal model delta sigma weight residual 119.90 97.31 22.59 3.00e+00 1.11e-01 5.67e+01 angle pdb=" O2B ADP M 401 " pdb=" PB ADP M 401 " pdb=" O3B ADP M 401 " ideal model delta sigma weight residual 119.90 98.13 21.77 3.00e+00 1.11e-01 5.27e+01 ... (remaining 141307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.92: 35110 30.92 - 61.84: 1561 61.84 - 92.76: 250 92.76 - 123.68: 10 123.68 - 154.60: 9 Dihedral angle restraints: 36940 sinusoidal: 20227 harmonic: 16713 Sorted by residual: dihedral pdb=" O1B ADP M 401 " pdb=" O3A ADP M 401 " pdb=" PB ADP M 401 " pdb=" PA ADP M 401 " ideal model delta sinusoidal sigma weight residual -60.00 94.60 -154.60 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O2A ADP Q 401 " pdb=" O3A ADP Q 401 " pdb=" PA ADP Q 401 " pdb=" PB ADP Q 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.97 -147.97 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O2A ADP O 401 " pdb=" O3A ADP O 401 " pdb=" PA ADP O 401 " pdb=" PB ADP O 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.05 -147.05 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 36937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4097 0.101 - 0.201: 1593 0.201 - 0.302: 267 0.302 - 0.403: 29 0.403 - 0.504: 4 Chirality restraints: 5990 Sorted by residual: 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 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA LYS F 150 " pdb=" N LYS F 150 " pdb=" C LYS F 150 " pdb=" CB LYS F 150 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA LYS F 128 " pdb=" N LYS F 128 " pdb=" C LYS F 128 " pdb=" CB LYS F 128 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 5987 not shown) Planarity restraints: 11609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 340 " -0.402 2.00e-02 2.50e+03 1.50e-01 9.01e+02 pdb=" CG TRP M 340 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP M 340 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP M 340 " 0.119 2.00e-02 2.50e+03 pdb=" NE1 TRP M 340 " 0.162 2.00e-02 2.50e+03 pdb=" CE2 TRP M 340 " 0.097 2.00e-02 2.50e+03 pdb=" CE3 TRP M 340 " 0.145 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 340 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 340 " 0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP M 340 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP M 340 " -0.076 2.00e-02 2.50e+03 pdb=" HE1 TRP M 340 " 0.106 2.00e-02 2.50e+03 pdb=" HE3 TRP M 340 " 0.183 2.00e-02 2.50e+03 pdb=" HZ2 TRP M 340 " -0.123 2.00e-02 2.50e+03 pdb=" HZ3 TRP M 340 " 0.016 2.00e-02 2.50e+03 pdb=" HH2 TRP M 340 " -0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 340 " -0.288 2.00e-02 2.50e+03 1.05e-01 4.40e+02 pdb=" CG TRP H 340 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP H 340 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP H 340 " 0.081 2.00e-02 2.50e+03 pdb=" NE1 TRP H 340 " 0.122 2.00e-02 2.50e+03 pdb=" CE2 TRP H 340 " 0.067 2.00e-02 2.50e+03 pdb=" CE3 TRP H 340 " 0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 340 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 340 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP H 340 " -0.041 2.00e-02 2.50e+03 pdb=" HD1 TRP H 340 " -0.046 2.00e-02 2.50e+03 pdb=" HE1 TRP H 340 " 0.082 2.00e-02 2.50e+03 pdb=" HE3 TRP H 340 " 0.113 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 340 " -0.134 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 340 " 0.019 2.00e-02 2.50e+03 pdb=" HH2 TRP H 340 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 340 " -0.282 2.00e-02 2.50e+03 1.03e-01 4.21e+02 pdb=" CG TRP R 340 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP R 340 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP R 340 " 0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP R 340 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 TRP R 340 " 0.055 2.00e-02 2.50e+03 pdb=" CE3 TRP R 340 " 0.091 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 340 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 340 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP R 340 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TRP R 340 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TRP R 340 " 0.089 2.00e-02 2.50e+03 pdb=" HE3 TRP R 340 " 0.121 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 340 " -0.109 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 340 " 0.022 2.00e-02 2.50e+03 pdb=" HH2 TRP R 340 " -0.133 2.00e-02 2.50e+03 ... (remaining 11606 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 5089 2.18 - 2.78: 138059 2.78 - 3.39: 226697 3.39 - 3.99: 308533 3.99 - 4.60: 452624 Nonbonded interactions: 1131002 Sorted by model distance: nonbonded pdb=" OD2 ASP A 185 " pdb=" H1 HOH A 601 " model vdw 1.570 2.450 nonbonded pdb=" HH TYR A 246 " pdb=" OE2 GLU A 254 " model vdw 1.579 2.450 nonbonded pdb=" OE1 GLU O 270 " pdb=" HG1 THR P 202 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP C 328 " pdb=" HG1 THR O 351 " model vdw 1.589 2.450 nonbonded pdb=" HG1 THR G 12 " pdb=" OE1 GLU G 13 " model vdw 1.590 2.450 ... (remaining 1130997 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)) 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)) 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)) selection = (chain 'N' and resid 6 through 375) 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)) 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)) 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)) 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)) } 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: 1.300 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: 1.050 Extract box with map and model: 2.080 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 128.830 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.240 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.012 0.144 39916 Z= 0.810 Angle : 1.910 23.514 54160 Z= 1.243 Chirality : 0.103 0.504 5990 Planarity : 0.018 0.403 6962 Dihedral : 15.069 154.603 14846 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 2.29 % Allowed : 5.69 % Favored : 92.02 % Cbeta Deviations : 0.17 % 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: -2.07 (0.11), residues: 4854 helix: -2.35 (0.09), residues: 1939 sheet: -0.65 (0.19), residues: 653 loop : -0.44 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.261 0.031 TRP M 340 HIS 0.015 0.004 HIS R 275 PHE 0.105 0.013 PHE D 196 TYR 0.181 0.019 TYR D 86 ARG 0.019 0.002 ARG D 255 *********************** 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 843 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 747 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: A 10 MET cc_start: 0.8999 (mtm) cc_final: 0.8521 (mtm) REVERT: A 130 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6279 (mt-10) REVERT: A 183 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7912 (p) REVERT: A 266 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 276 HIS cc_start: 0.7315 (p90) cc_final: 0.7046 (p90) REVERT: A 321 ASP cc_start: 0.7949 (m-30) cc_final: 0.7745 (t0) REVERT: A 341 ASN cc_start: 0.8079 (t0) cc_final: 0.7465 (t0) REVERT: B 21 LYS cc_start: 0.8504 (mtmt) cc_final: 0.7813 (mmmt) REVERT: B 81 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 224 GLU cc_start: 0.7941 (pt0) cc_final: 0.7484 (mp0) REVERT: B 237 MET cc_start: 0.8716 (mmm) cc_final: 0.8482 (mmm) REVERT: B 249 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8047 (mttm) REVERT: B 295 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7356 (ttp80) REVERT: B 305 MET cc_start: 0.9147 (mmm) cc_final: 0.8898 (mmt) REVERT: C 16 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7958 (tp30) REVERT: C 89 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7622 (p) REVERT: C 100 ASN cc_start: 0.8235 (t0) cc_final: 0.7854 (t0) REVERT: C 157 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7309 (p0) REVERT: C 159 VAL cc_start: 0.8899 (t) cc_final: 0.8619 (m) REVERT: C 167 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8023 (p0) REVERT: C 183 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8041 (mmmm) REVERT: C 262 GLU cc_start: 0.7692 (pt0) cc_final: 0.7387 (tp30) REVERT: D 1 MET cc_start: 0.8723 (ptt) cc_final: 0.8504 (ptt) REVERT: D 106 GLN cc_start: 0.7615 (pt0) cc_final: 0.7346 (tm-30) REVERT: D 206 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7457 (mtt90) REVERT: D 215 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8415 (p) REVERT: D 225 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: D 230 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7532 (pt0) REVERT: D 247 GLU cc_start: 0.7917 (tp30) cc_final: 0.7554 (tp30) REVERT: D 286 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7830 (tptp) REVERT: E 79 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7278 (mt-10) REVERT: E 94 ARG cc_start: 0.7674 (mtp-110) cc_final: 0.7207 (mtm-85) REVERT: E 115 ASN cc_start: 0.8181 (t0) cc_final: 0.7951 (t0) REVERT: E 125 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: E 156 HIS cc_start: 0.8046 (t-90) cc_final: 0.7765 (t-90) REVERT: E 166 LYS cc_start: 0.7623 (mtpm) cc_final: 0.7381 (mmtt) REVERT: F 1 MET cc_start: 0.6103 (tmm) cc_final: 0.5784 (tmm) REVERT: F 84 ARG cc_start: 0.6910 (mtt-85) cc_final: 0.6695 (mtp-110) REVERT: F 88 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.7227 (ttt-90) REVERT: F 107 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7750 (mtpp) REVERT: G 19 GLN cc_start: 0.7899 (pm20) cc_final: 0.7561 (pm20) REVERT: G 88 ARG cc_start: 0.7705 (mmp80) cc_final: 0.7033 (mtm110) REVERT: G 124 SER cc_start: 0.8514 (t) cc_final: 0.8079 (m) REVERT: G 132 LYS cc_start: 0.8352 (mttm) cc_final: 0.8124 (mmtt) REVERT: H 68 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7295 (mtmm) REVERT: H 100 GLU cc_start: 0.7522 (tt0) cc_final: 0.6959 (tm-30) REVERT: H 194 THR cc_start: 0.8668 (t) cc_final: 0.8456 (p) REVERT: H 227 MET cc_start: 0.8432 (mmm) cc_final: 0.8150 (mmm) REVERT: H 289 ILE cc_start: 0.8342 (mt) cc_final: 0.8070 (mt) REVERT: I 44 MET cc_start: 0.8768 (mtp) cc_final: 0.8364 (mtm) REVERT: I 149 THR cc_start: 0.5854 (m) cc_final: 0.5462 (t) REVERT: I 194 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8504 (p) REVERT: I 280 ASN cc_start: 0.7980 (m-40) cc_final: 0.7532 (m-40) REVERT: I 305 MET cc_start: 0.8426 (mmm) cc_final: 0.8159 (mmm) REVERT: M 119 MET cc_start: 0.8193 (ttm) cc_final: 0.7525 (ttm) REVERT: M 123 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.6918 (mpt) REVERT: M 337 TYR cc_start: 0.8191 (m-80) cc_final: 0.7894 (m-10) REVERT: N 54 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7812 (m) REVERT: N 176 MET cc_start: 0.7868 (mtp) cc_final: 0.7631 (mtp) REVERT: N 270 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7880 (tt0) REVERT: O 81 ASP cc_start: 0.8426 (m-30) cc_final: 0.8152 (m-30) REVERT: O 82 MET cc_start: 0.8743 (tpt) cc_final: 0.8233 (tpt) REVERT: O 118 LYS cc_start: 0.7752 (mttm) cc_final: 0.7296 (mtpp) REVERT: O 132 MET cc_start: 0.8614 (ppp) cc_final: 0.8345 (ptm) REVERT: O 195 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: O 206 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7258 (ttm-80) REVERT: O 210 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7187 (ttp80) REVERT: O 222 ASP cc_start: 0.7932 (t0) cc_final: 0.7621 (p0) REVERT: O 227 MET cc_start: 0.8417 (tpt) cc_final: 0.8198 (mmm) REVERT: O 283 MET cc_start: 0.8899 (mmm) cc_final: 0.8498 (mmt) REVERT: O 287 ILE cc_start: 0.8489 (tt) cc_final: 0.8106 (mt) REVERT: O 289 ILE cc_start: 0.8729 (pt) cc_final: 0.8461 (pt) REVERT: O 292 ASP cc_start: 0.8273 (m-30) cc_final: 0.8031 (m-30) REVERT: O 305 MET cc_start: 0.8803 (mmm) cc_final: 0.8497 (mmm) REVERT: O 325 MET cc_start: 0.7962 (ptm) cc_final: 0.7597 (ptm) REVERT: O 326 LYS cc_start: 0.7906 (ptpp) cc_final: 0.7665 (mmtt) REVERT: O 328 LYS cc_start: 0.7556 (mtmt) cc_final: 0.7103 (mmmt) REVERT: O 372 ARG cc_start: 0.8435 (ptt-90) cc_final: 0.8081 (mtm110) REVERT: P 71 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8250 (mt) REVERT: P 72 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7161 (tt0) REVERT: P 81 ASP cc_start: 0.8203 (m-30) cc_final: 0.7877 (m-30) REVERT: P 82 MET cc_start: 0.9156 (tpt) cc_final: 0.8796 (tpt) REVERT: P 119 MET cc_start: 0.8217 (ttp) cc_final: 0.7887 (ttp) REVERT: P 194 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7757 (p) REVERT: P 205 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7393 (mt-10) REVERT: P 227 MET cc_start: 0.8725 (mmm) cc_final: 0.8192 (mmm) REVERT: P 313 MET cc_start: 0.8789 (tpt) cc_final: 0.8560 (mmm) REVERT: Q 9 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8607 (p) REVERT: Q 41 GLN cc_start: 0.6748 (mm-40) cc_final: 0.6341 (tp40) REVERT: Q 44 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8053 (mpt) REVERT: Q 49 GLN cc_start: 0.7542 (tt0) cc_final: 0.7151 (mm-40) REVERT: Q 54 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9019 (t) REVERT: Q 105 LEU cc_start: 0.8522 (mt) cc_final: 0.8143 (mt) REVERT: Q 121 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7073 (tt0) REVERT: Q 177 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8495 (tmt170) REVERT: Q 269 MET cc_start: 0.8721 (ptm) cc_final: 0.8463 (ptm) REVERT: Q 277 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8653 (t) REVERT: Q 284 LYS cc_start: 0.7937 (mttm) cc_final: 0.7603 (mtpt) REVERT: Q 291 LYS cc_start: 0.6205 (mttm) cc_final: 0.5601 (mmtt) REVERT: Q 326 LYS cc_start: 0.8067 (pttt) cc_final: 0.7801 (mmmm) REVERT: Q 328 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7419 (tptt) REVERT: R 116 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7579 (mtp85) REVERT: R 227 MET cc_start: 0.8480 (mmm) cc_final: 0.8080 (mmm) REVERT: R 283 MET cc_start: 0.8796 (mmm) cc_final: 0.8453 (mmm) REVERT: R 286 ASP cc_start: 0.7468 (m-30) cc_final: 0.7082 (t0) REVERT: R 291 LYS cc_start: 0.8530 (ttpp) cc_final: 0.8043 (mmtp) REVERT: R 352 PHE cc_start: 0.8671 (t80) cc_final: 0.8184 (t80) outliers start: 96 outliers final: 28 residues processed: 811 average time/residue: 1.1793 time to fit residues: 1472.3220 Evaluate side-chains 537 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 489 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain E residue 2 PRO Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 85 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain M residue 123 MET Chi-restraints excluded: chain M residue 214 GLU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain O residue 12 ASN Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 194 THR Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 177 ARG Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 2.9990 chunk 370 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 383 optimal weight: 0.9980 chunk 148 optimal weight: 0.0670 chunk 233 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 0.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 382 GLN B 83 ASN B 363 GLN C 251 GLN D 233 GLN F 60 GLN F 92 GLN G 48 GLN G 106 ASN I 246 GLN M 88 HIS N 296 ASN O 162 ASN P 128 ASN Q 246 GLN R 49 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094993 restraints weight = 173031.345| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.62 r_work: 0.3055 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 39916 Z= 0.244 Angle : 0.746 9.088 54160 Z= 0.397 Chirality : 0.047 0.226 5990 Planarity : 0.007 0.151 6962 Dihedral : 10.892 157.047 5625 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.86 % Allowed : 8.72 % Favored : 89.42 % 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: -1.18 (0.12), residues: 4854 helix: -1.27 (0.11), residues: 1963 sheet: -0.81 (0.16), residues: 943 loop : 0.10 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 356 HIS 0.007 0.001 HIS A 404 PHE 0.025 0.002 PHE B 277 TYR 0.021 0.001 TYR B 88 ARG 0.007 0.001 ARG Q 206 *********************** 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 587 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 509 time to evaluate : 4.742 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: A 73 ASP cc_start: 0.8104 (t0) cc_final: 0.7761 (t0) REVERT: A 160 GLN cc_start: 0.7996 (pt0) cc_final: 0.7059 (pt0) REVERT: A 183 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 276 HIS cc_start: 0.7770 (p90) cc_final: 0.7372 (p90) REVERT: A 341 ASN cc_start: 0.8255 (t0) cc_final: 0.7346 (t0) REVERT: B 21 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8161 (mmmt) REVERT: B 224 GLU cc_start: 0.8266 (pt0) cc_final: 0.8025 (mt-10) REVERT: B 237 MET cc_start: 0.9152 (mmm) cc_final: 0.8951 (mmm) REVERT: B 255 TYR cc_start: 0.8996 (p90) cc_final: 0.8605 (p90) REVERT: B 294 TYR cc_start: 0.9095 (m-80) cc_final: 0.8889 (m-80) REVERT: B 295 ARG cc_start: 0.8025 (mtp180) cc_final: 0.7789 (ttp80) REVERT: C 55 ASP cc_start: 0.8244 (t0) cc_final: 0.7820 (m-30) REVERT: C 157 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7436 (p0) REVERT: C 327 MET cc_start: 0.8357 (tpp) cc_final: 0.8004 (tpt) REVERT: D 103 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7681 (mt-10) REVERT: D 113 MET cc_start: 0.9116 (tpp) cc_final: 0.8348 (mmt) REVERT: D 117 ASN cc_start: 0.8353 (m-40) cc_final: 0.8046 (m-40) REVERT: D 206 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7926 (mtt90) REVERT: D 215 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8932 (t) REVERT: D 247 GLU cc_start: 0.8431 (tp30) cc_final: 0.8141 (tp30) REVERT: E 79 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7886 (mt-10) REVERT: E 94 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7697 (mtm-85) REVERT: E 115 ASN cc_start: 0.8852 (t0) cc_final: 0.8473 (t0) REVERT: E 156 HIS cc_start: 0.8083 (t-90) cc_final: 0.7761 (t-90) REVERT: E 170 MET cc_start: 0.9076 (mmt) cc_final: 0.8750 (mmt) REVERT: F 77 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8402 (ttpt) REVERT: G 30 GLU cc_start: 0.8221 (mp0) cc_final: 0.7749 (tm-30) REVERT: G 88 ARG cc_start: 0.7860 (mmp80) cc_final: 0.7478 (mtm110) REVERT: G 124 SER cc_start: 0.8779 (t) cc_final: 0.8474 (m) REVERT: H 68 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8052 (mttp) REVERT: H 100 GLU cc_start: 0.7413 (tt0) cc_final: 0.7061 (tm-30) REVERT: H 107 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7314 (tm-30) REVERT: H 119 MET cc_start: 0.8472 (ttm) cc_final: 0.8231 (ttp) REVERT: H 169 TYR cc_start: 0.8337 (m-80) cc_final: 0.8070 (m-10) REVERT: I 44 MET cc_start: 0.8589 (mtp) cc_final: 0.8367 (mtm) REVERT: I 132 MET cc_start: 0.7653 (pmm) cc_final: 0.7330 (pmm) REVERT: I 194 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8798 (p) REVERT: I 280 ASN cc_start: 0.7993 (m-40) cc_final: 0.7742 (m-40) REVERT: I 283 MET cc_start: 0.8450 (tpp) cc_final: 0.7903 (tpp) REVERT: M 90 PHE cc_start: 0.8275 (m-80) cc_final: 0.7620 (m-80) REVERT: M 167 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7052 (tm-30) REVERT: N 54 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7910 (m) REVERT: N 270 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7925 (tt0) REVERT: O 82 MET cc_start: 0.9269 (tpt) cc_final: 0.9012 (tpt) REVERT: O 118 LYS cc_start: 0.8567 (mttm) cc_final: 0.8270 (mtpp) REVERT: O 210 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8237 (ttp80) REVERT: O 222 ASP cc_start: 0.8223 (t0) cc_final: 0.7986 (p0) REVERT: O 283 MET cc_start: 0.9037 (mmm) cc_final: 0.8710 (mmt) REVERT: O 287 ILE cc_start: 0.8669 (tt) cc_final: 0.8402 (mt) REVERT: O 305 MET cc_start: 0.8933 (mmm) cc_final: 0.8676 (mmm) REVERT: O 325 MET cc_start: 0.8122 (ptm) cc_final: 0.7674 (ptm) REVERT: P 82 MET cc_start: 0.9366 (tpt) cc_final: 0.9104 (tpt) REVERT: P 119 MET cc_start: 0.8363 (ttp) cc_final: 0.8002 (ttp) REVERT: P 227 MET cc_start: 0.8779 (mmm) cc_final: 0.8373 (mmm) REVERT: Q 44 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.7977 (mpt) REVERT: Q 47 MET cc_start: 0.8390 (mmm) cc_final: 0.7670 (ptt) REVERT: Q 54 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.9301 (t) REVERT: Q 103 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8737 (p) REVERT: Q 269 MET cc_start: 0.8829 (ptm) cc_final: 0.8553 (ptm) REVERT: Q 277 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8936 (t) REVERT: Q 291 LYS cc_start: 0.6729 (mttm) cc_final: 0.6249 (mmtt) REVERT: R 82 MET cc_start: 0.8777 (mmm) cc_final: 0.7834 (tpt) REVERT: R 175 ILE cc_start: 0.8951 (mt) cc_final: 0.8699 (mt) REVERT: R 286 ASP cc_start: 0.7813 (m-30) cc_final: 0.7479 (t0) REVERT: R 291 LYS cc_start: 0.8837 (ttpp) cc_final: 0.8462 (mmtt) REVERT: R 352 PHE cc_start: 0.8748 (t80) cc_final: 0.8343 (t80) outliers start: 78 outliers final: 41 residues processed: 564 average time/residue: 1.1668 time to fit residues: 1022.5326 Evaluate side-chains 455 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 404 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 177 ARG Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 358 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 179 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 378 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 140 HIS C 196 ASN D 292 GLN E 40 GLN E 139 GLN G 147 ASN H 162 ASN M 297 ASN M 314 GLN O 360 GLN O 371 HIS ** Q 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091536 restraints weight = 175008.270| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.61 r_work: 0.3002 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 39916 Z= 0.356 Angle : 0.669 8.152 54160 Z= 0.347 Chirality : 0.046 0.211 5990 Planarity : 0.005 0.057 6962 Dihedral : 9.838 174.536 5580 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.00 % Allowed : 9.77 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.12), residues: 4854 helix: -0.81 (0.11), residues: 1998 sheet: -0.98 (0.17), residues: 897 loop : -0.02 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 356 HIS 0.007 0.001 HIS A 404 PHE 0.021 0.002 PHE B 277 TYR 0.018 0.001 TYR B 88 ARG 0.008 0.001 ARG I 290 *********************** 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 510 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 426 time to evaluate : 4.618 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: A 137 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 148 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8158 (mt-10) REVERT: A 262 PRO cc_start: 0.8810 (Cg_endo) cc_final: 0.8581 (Cg_exo) REVERT: A 276 HIS cc_start: 0.7620 (p90) cc_final: 0.7401 (p90) REVERT: B 6 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7740 (mt) REVERT: B 21 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8092 (mmmt) REVERT: B 72 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7305 (tt0) REVERT: B 255 TYR cc_start: 0.9069 (p90) cc_final: 0.8718 (p90) REVERT: B 295 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7672 (ttm170) REVERT: B 361 MET cc_start: 0.8649 (ptp) cc_final: 0.8188 (ptm) REVERT: C 55 ASP cc_start: 0.8429 (t0) cc_final: 0.8041 (m-30) REVERT: C 157 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7586 (p0) REVERT: D 23 ASN cc_start: 0.8627 (p0) cc_final: 0.8389 (p0) REVERT: D 117 ASN cc_start: 0.8448 (m-40) cc_final: 0.8092 (m-40) REVERT: D 206 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7880 (mtt90) REVERT: D 247 GLU cc_start: 0.8420 (tp30) cc_final: 0.8098 (tp30) REVERT: E 79 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7943 (mt-10) REVERT: E 94 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7639 (mtm-85) REVERT: E 115 ASN cc_start: 0.8763 (t0) cc_final: 0.8451 (t0) REVERT: E 156 HIS cc_start: 0.8011 (t-90) cc_final: 0.7763 (t-90) REVERT: F 77 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8517 (ttpt) REVERT: F 88 ARG cc_start: 0.8292 (ttt-90) cc_final: 0.7921 (ttt-90) REVERT: G 30 GLU cc_start: 0.8208 (mp0) cc_final: 0.7818 (tm-30) REVERT: G 88 ARG cc_start: 0.7927 (mmp80) cc_final: 0.7503 (mtm110) REVERT: G 124 SER cc_start: 0.8745 (t) cc_final: 0.8459 (m) REVERT: H 100 GLU cc_start: 0.7363 (tt0) cc_final: 0.6989 (tm-30) REVERT: I 125 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7314 (mt-10) REVERT: I 280 ASN cc_start: 0.8093 (m-40) cc_final: 0.7859 (m-40) REVERT: M 72 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: M 90 PHE cc_start: 0.8188 (m-80) cc_final: 0.7614 (m-80) REVERT: M 167 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7421 (tm-30) REVERT: M 207 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8362 (mm-30) REVERT: M 211 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: M 287 ILE cc_start: 0.8448 (tp) cc_final: 0.8132 (tt) REVERT: N 54 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7989 (m) REVERT: N 270 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7959 (tt0) REVERT: O 118 LYS cc_start: 0.8605 (mttm) cc_final: 0.8298 (mtpp) REVERT: O 222 ASP cc_start: 0.8275 (t0) cc_final: 0.7978 (p0) REVERT: O 283 MET cc_start: 0.9062 (mmm) cc_final: 0.8801 (mmt) REVERT: O 287 ILE cc_start: 0.8742 (tt) cc_final: 0.8444 (mt) REVERT: O 305 MET cc_start: 0.8848 (mmm) cc_final: 0.8320 (mmt) REVERT: O 325 MET cc_start: 0.8153 (ptm) cc_final: 0.7661 (ptm) REVERT: O 360 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: P 82 MET cc_start: 0.9342 (tpt) cc_final: 0.9130 (tpt) REVERT: P 227 MET cc_start: 0.8669 (mmm) cc_final: 0.8342 (mmm) REVERT: Q 44 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.7913 (mpt) REVERT: Q 47 MET cc_start: 0.8486 (mmm) cc_final: 0.7728 (ptt) REVERT: Q 54 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9312 (t) REVERT: Q 103 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8667 (p) REVERT: Q 177 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8658 (ttt180) REVERT: Q 269 MET cc_start: 0.8947 (ptm) cc_final: 0.8733 (ptm) REVERT: Q 291 LYS cc_start: 0.6523 (mttm) cc_final: 0.5532 (mmtt) REVERT: R 283 MET cc_start: 0.8833 (mmm) cc_final: 0.8131 (mmp) REVERT: R 286 ASP cc_start: 0.7764 (m-30) cc_final: 0.7411 (t0) REVERT: R 291 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8456 (mmtt) REVERT: R 352 PHE cc_start: 0.8748 (t80) cc_final: 0.8269 (t80) outliers start: 84 outliers final: 53 residues processed: 494 average time/residue: 1.0824 time to fit residues: 841.3643 Evaluate side-chains 445 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 381 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain M residue 314 GLN Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 328 LYS Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain O residue 360 GLN Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 54 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 177 ARG Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 350 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 392 optimal weight: 3.9990 chunk 427 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 384 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 304 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 433 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS A 160 GLN ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS M 314 GLN O 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.090337 restraints weight = 174090.969| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.60 r_work: 0.3004 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 39916 Z= 0.314 Angle : 0.628 7.746 54160 Z= 0.322 Chirality : 0.045 0.191 5990 Planarity : 0.004 0.048 6962 Dihedral : 9.448 173.000 5576 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.83 % Allowed : 10.65 % Favored : 87.52 % 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: -0.86 (0.12), residues: 4854 helix: -0.59 (0.11), residues: 2000 sheet: -1.09 (0.16), residues: 909 loop : 0.02 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 356 HIS 0.007 0.001 HIS A 404 PHE 0.019 0.001 PHE B 277 TYR 0.016 0.001 TYR B 88 ARG 0.004 0.000 ARG P 28 *********************** 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 469 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 392 time to evaluate : 4.701 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: A 148 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 276 HIS cc_start: 0.7943 (p90) cc_final: 0.7283 (p90) REVERT: B 6 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7733 (mt) REVERT: B 72 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7131 (tt0) REVERT: B 255 TYR cc_start: 0.9115 (p90) cc_final: 0.8797 (p90) REVERT: B 295 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7656 (ttm170) REVERT: B 361 MET cc_start: 0.8565 (ptp) cc_final: 0.8173 (ptm) REVERT: C 55 ASP cc_start: 0.8352 (t0) cc_final: 0.7987 (m-30) REVERT: C 157 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7584 (p0) REVERT: D 23 ASN cc_start: 0.8664 (p0) cc_final: 0.8438 (p0) REVERT: D 117 ASN cc_start: 0.8556 (m-40) cc_final: 0.8142 (m-40) REVERT: D 206 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7972 (mtt90) REVERT: D 247 GLU cc_start: 0.8478 (tp30) cc_final: 0.8166 (tp30) REVERT: E 94 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7692 (mtm-85) REVERT: E 115 ASN cc_start: 0.8684 (t0) cc_final: 0.8428 (t0) REVERT: F 88 ARG cc_start: 0.8241 (ttt-90) cc_final: 0.7867 (ttt-90) REVERT: G 30 GLU cc_start: 0.8190 (mp0) cc_final: 0.7838 (tm-30) REVERT: G 88 ARG cc_start: 0.7950 (mmp80) cc_final: 0.7527 (mtm110) REVERT: G 124 SER cc_start: 0.8707 (t) cc_final: 0.8479 (m) REVERT: H 68 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8008 (mttp) REVERT: H 100 GLU cc_start: 0.7343 (tt0) cc_final: 0.6984 (tm-30) REVERT: I 355 MET cc_start: 0.7813 (tpp) cc_final: 0.7590 (mtt) REVERT: M 72 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: M 167 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7422 (tm-30) REVERT: M 207 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8313 (mm-30) REVERT: M 279 TYR cc_start: 0.9015 (t80) cc_final: 0.8726 (t80) REVERT: N 54 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8079 (m) REVERT: O 118 LYS cc_start: 0.8615 (mttm) cc_final: 0.8305 (mtpp) REVERT: O 283 MET cc_start: 0.9019 (mmm) cc_final: 0.8759 (mmt) REVERT: O 287 ILE cc_start: 0.8922 (tt) cc_final: 0.8459 (mt) REVERT: Q 44 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.7954 (mpt) REVERT: Q 47 MET cc_start: 0.8443 (mmm) cc_final: 0.7779 (ptt) REVERT: Q 54 VAL cc_start: 0.9569 (p) cc_final: 0.9312 (t) REVERT: Q 103 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8639 (p) REVERT: Q 291 LYS cc_start: 0.6589 (mttm) cc_final: 0.5890 (mmtt) REVERT: R 283 MET cc_start: 0.8750 (mmm) cc_final: 0.8047 (mmp) REVERT: R 286 ASP cc_start: 0.7757 (m-30) cc_final: 0.7413 (t0) REVERT: R 291 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8488 (mmtt) REVERT: R 352 PHE cc_start: 0.8708 (t80) cc_final: 0.8292 (t80) outliers start: 77 outliers final: 54 residues processed: 451 average time/residue: 1.1230 time to fit residues: 797.1453 Evaluate side-chains 438 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 377 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 211 ASP Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 227 MET Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 137 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 203 optimal weight: 0.0970 chunk 323 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 414 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 363 optimal weight: 7.9990 chunk 480 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 ASN N 162 ASN O 360 GLN Q 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097856 restraints weight = 177157.110| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.92 r_work: 0.3120 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39916 Z= 0.193 Angle : 0.572 7.134 54160 Z= 0.288 Chirality : 0.043 0.158 5990 Planarity : 0.004 0.051 6962 Dihedral : 8.803 153.240 5563 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 11.22 % Favored : 87.18 % 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: -0.24 (0.12), residues: 1998 sheet: -0.94 (0.16), residues: 951 loop : 0.13 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 356 HIS 0.006 0.001 HIS A 404 PHE 0.017 0.001 PHE B 277 TYR 0.013 0.001 TYR B 88 ARG 0.005 0.000 ARG Q 177 *********************** 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 472 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 405 time to evaluate : 4.685 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: A 130 GLU cc_start: 0.7869 (pm20) cc_final: 0.7456 (pm20) REVERT: A 137 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: A 148 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 188 ASP cc_start: 0.8728 (t0) cc_final: 0.7720 (t0) REVERT: A 276 HIS cc_start: 0.8011 (p90) cc_final: 0.7313 (p90) REVERT: B 72 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7266 (tt0) REVERT: B 102 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7385 (ptpp) REVERT: B 295 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7670 (ttm170) REVERT: B 361 MET cc_start: 0.8493 (ptp) cc_final: 0.8116 (ptm) REVERT: C 55 ASP cc_start: 0.8455 (t0) cc_final: 0.8018 (m-30) REVERT: C 157 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7678 (p0) REVERT: D 23 ASN cc_start: 0.8719 (p0) cc_final: 0.8499 (p0) REVERT: D 117 ASN cc_start: 0.8652 (m-40) cc_final: 0.8228 (m-40) REVERT: D 206 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7904 (mtm110) REVERT: D 247 GLU cc_start: 0.8555 (tp30) cc_final: 0.8252 (tp30) REVERT: D 279 TYR cc_start: 0.9054 (t80) cc_final: 0.8806 (t80) REVERT: E 115 ASN cc_start: 0.8572 (t0) cc_final: 0.8362 (t0) REVERT: E 156 HIS cc_start: 0.7923 (t-90) cc_final: 0.7704 (t70) REVERT: F 88 ARG cc_start: 0.8261 (ttt-90) cc_final: 0.7877 (ttt-90) REVERT: G 30 GLU cc_start: 0.8262 (mp0) cc_final: 0.7788 (tm-30) REVERT: G 88 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7244 (mtm110) REVERT: G 124 SER cc_start: 0.8708 (t) cc_final: 0.8468 (m) REVERT: H 68 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7885 (mttm) REVERT: H 100 GLU cc_start: 0.7342 (tt0) cc_final: 0.7052 (tm-30) REVERT: M 72 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: M 167 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7370 (tm-30) REVERT: M 205 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8479 (pm20) REVERT: M 279 TYR cc_start: 0.8967 (t80) cc_final: 0.8631 (t80) REVERT: N 54 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7932 (m) REVERT: O 118 LYS cc_start: 0.8595 (mttm) cc_final: 0.8246 (mtpp) REVERT: O 283 MET cc_start: 0.8997 (mmm) cc_final: 0.8732 (mmt) REVERT: O 287 ILE cc_start: 0.8876 (tt) cc_final: 0.8409 (mt) REVERT: P 82 MET cc_start: 0.9116 (tpt) cc_final: 0.8838 (tpp) REVERT: Q 44 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.7950 (mpt) REVERT: Q 47 MET cc_start: 0.8630 (mmm) cc_final: 0.7707 (ptt) REVERT: Q 54 VAL cc_start: 0.9599 (p) cc_final: 0.9330 (t) REVERT: Q 291 LYS cc_start: 0.6523 (mttm) cc_final: 0.5811 (mmtt) REVERT: Q 372 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7572 (ptt90) REVERT: R 283 MET cc_start: 0.8655 (mmm) cc_final: 0.7947 (mmp) REVERT: R 286 ASP cc_start: 0.7735 (m-30) cc_final: 0.7320 (t0) REVERT: R 291 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8429 (mmtt) REVERT: R 352 PHE cc_start: 0.8674 (t80) cc_final: 0.8111 (t80) outliers start: 67 outliers final: 48 residues processed: 458 average time/residue: 1.1456 time to fit residues: 844.1336 Evaluate side-chains 442 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 386 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 162 ASN Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 82 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 486 optimal weight: 8.9990 chunk 407 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 475 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 417 optimal weight: 0.2980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS H 87 HIS O 360 GLN Q 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096358 restraints weight = 177856.511| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.92 r_work: 0.3093 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 39916 Z= 0.311 Angle : 0.594 7.101 54160 Z= 0.301 Chirality : 0.044 0.173 5990 Planarity : 0.004 0.054 6962 Dihedral : 8.719 152.582 5559 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.67 % Allowed : 11.46 % Favored : 86.87 % 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: -0.56 (0.12), residues: 4854 helix: -0.21 (0.12), residues: 2008 sheet: -1.02 (0.17), residues: 865 loop : 0.05 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 356 HIS 0.007 0.001 HIS A 404 PHE 0.018 0.001 PHE B 277 TYR 0.019 0.001 TYR B 255 ARG 0.004 0.000 ARG I 372 *********************** 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 453 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 383 time to evaluate : 4.679 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: A 130 GLU cc_start: 0.7896 (pm20) cc_final: 0.7472 (pm20) REVERT: A 137 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: A 188 ASP cc_start: 0.8768 (t70) cc_final: 0.7977 (t0) REVERT: A 276 HIS cc_start: 0.8019 (p90) cc_final: 0.7262 (p90) REVERT: A 363 MET cc_start: 0.8308 (mmp) cc_final: 0.7672 (mtp) REVERT: B 66 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8251 (tp40) REVERT: B 72 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7299 (tt0) REVERT: B 102 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7464 (ptpp) REVERT: B 295 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7727 (ttm170) REVERT: B 361 MET cc_start: 0.8542 (ptp) cc_final: 0.8160 (ptm) REVERT: C 55 ASP cc_start: 0.8450 (t0) cc_final: 0.7920 (m-30) REVERT: C 157 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7665 (p0) REVERT: D 117 ASN cc_start: 0.8683 (m-40) cc_final: 0.8121 (m110) REVERT: D 206 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.7958 (mtm110) REVERT: D 247 GLU cc_start: 0.8536 (tp30) cc_final: 0.8227 (tp30) REVERT: F 74 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8819 (pt) REVERT: F 88 ARG cc_start: 0.8362 (ttt-90) cc_final: 0.7969 (ttt-90) REVERT: G 30 GLU cc_start: 0.8290 (mp0) cc_final: 0.7846 (tm-30) REVERT: G 88 ARG cc_start: 0.7975 (mmp80) cc_final: 0.7278 (mtm110) REVERT: G 124 SER cc_start: 0.8741 (t) cc_final: 0.8508 (m) REVERT: H 68 LYS cc_start: 0.8633 (ptmt) cc_final: 0.7915 (mttm) REVERT: H 100 GLU cc_start: 0.7387 (tt0) cc_final: 0.7105 (tm-30) REVERT: M 72 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: M 123 MET cc_start: 0.8861 (mmt) cc_final: 0.8397 (mmt) REVERT: M 167 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7600 (tm-30) REVERT: M 279 TYR cc_start: 0.8984 (t80) cc_final: 0.8634 (t80) REVERT: N 54 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7989 (m) REVERT: O 283 MET cc_start: 0.9023 (mmm) cc_final: 0.8763 (mmt) REVERT: O 287 ILE cc_start: 0.8922 (tt) cc_final: 0.8495 (mt) REVERT: P 82 MET cc_start: 0.9123 (tpt) cc_final: 0.8845 (tpp) REVERT: Q 44 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.7856 (mpt) REVERT: Q 47 MET cc_start: 0.8659 (mmm) cc_final: 0.7741 (ptt) REVERT: Q 54 VAL cc_start: 0.9607 (p) cc_final: 0.9320 (t) REVERT: Q 103 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8604 (p) REVERT: Q 291 LYS cc_start: 0.6454 (mttm) cc_final: 0.5723 (mmtt) REVERT: Q 372 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7527 (ptt90) REVERT: R 75 ILE cc_start: 0.8563 (pt) cc_final: 0.8299 (pt) REVERT: R 283 MET cc_start: 0.8721 (mmm) cc_final: 0.8019 (mmp) REVERT: R 286 ASP cc_start: 0.7740 (m-30) cc_final: 0.7336 (t0) REVERT: R 291 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8448 (mmtt) REVERT: R 352 PHE cc_start: 0.8678 (t80) cc_final: 0.8120 (t80) outliers start: 70 outliers final: 53 residues processed: 441 average time/residue: 1.0764 time to fit residues: 752.3853 Evaluate side-chains 434 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 371 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 194 THR 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 318 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 361 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 450 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 434 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS E 115 ASN E 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096573 restraints weight = 177629.861| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.92 r_work: 0.3100 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 39916 Z= 0.254 Angle : 0.576 7.057 54160 Z= 0.290 Chirality : 0.044 0.160 5990 Planarity : 0.004 0.051 6962 Dihedral : 8.538 152.001 5559 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.93 % Allowed : 11.36 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 4854 helix: -0.09 (0.12), residues: 2016 sheet: -0.84 (0.16), residues: 944 loop : 0.09 (0.15), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 356 HIS 0.009 0.001 HIS E 156 PHE 0.016 0.001 PHE B 277 TYR 0.017 0.001 TYR B 255 ARG 0.006 0.000 ARG P 28 *********************** 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 466 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 385 time to evaluate : 4.755 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: A 130 GLU cc_start: 0.7876 (pm20) cc_final: 0.7455 (pm20) REVERT: A 137 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 148 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8101 (mt-10) REVERT: A 176 ASP cc_start: 0.7371 (m-30) cc_final: 0.7128 (m-30) REVERT: A 188 ASP cc_start: 0.8740 (t70) cc_final: 0.7970 (t0) REVERT: A 276 HIS cc_start: 0.7921 (p90) cc_final: 0.7145 (p90) REVERT: A 363 MET cc_start: 0.8275 (mmp) cc_final: 0.7693 (mtp) REVERT: B 66 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: B 102 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7429 (ptpp) REVERT: B 295 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7650 (ttm170) REVERT: B 361 MET cc_start: 0.8589 (ptp) cc_final: 0.8202 (ptm) REVERT: C 55 ASP cc_start: 0.8459 (t0) cc_final: 0.7922 (m-30) REVERT: C 157 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7649 (p0) REVERT: D 117 ASN cc_start: 0.8634 (m-40) cc_final: 0.8166 (m110) REVERT: D 206 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.7983 (mtm110) REVERT: D 247 GLU cc_start: 0.8509 (tp30) cc_final: 0.8205 (tp30) REVERT: D 279 TYR cc_start: 0.8982 (t80) cc_final: 0.8669 (t80) REVERT: E 94 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7210 (mtm-85) REVERT: F 74 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8807 (pt) REVERT: F 88 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.7880 (ttt-90) REVERT: G 30 GLU cc_start: 0.8291 (mp0) cc_final: 0.7851 (tm-30) REVERT: G 88 ARG cc_start: 0.8013 (mmp80) cc_final: 0.7283 (mtp85) REVERT: G 124 SER cc_start: 0.8722 (t) cc_final: 0.8497 (m) REVERT: H 12 ASN cc_start: 0.8322 (m-40) cc_final: 0.8120 (m-40) REVERT: H 68 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7963 (mttm) REVERT: H 100 GLU cc_start: 0.7407 (tt0) cc_final: 0.7096 (tm-30) REVERT: I 125 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7269 (mt-10) REVERT: I 305 MET cc_start: 0.8793 (mmm) cc_final: 0.8587 (mmm) REVERT: M 72 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: M 123 MET cc_start: 0.8870 (mmt) cc_final: 0.8510 (mmt) REVERT: M 167 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7598 (tm-30) REVERT: M 279 TYR cc_start: 0.8966 (t80) cc_final: 0.8600 (t80) REVERT: O 283 MET cc_start: 0.9012 (mmm) cc_final: 0.8760 (mmt) REVERT: O 287 ILE cc_start: 0.8922 (tt) cc_final: 0.8509 (mt) REVERT: P 313 MET cc_start: 0.8527 (mmm) cc_final: 0.8202 (mmm) REVERT: Q 44 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.7841 (mpt) REVERT: Q 47 MET cc_start: 0.8653 (mmm) cc_final: 0.7756 (ptt) REVERT: Q 54 VAL cc_start: 0.9605 (p) cc_final: 0.9305 (t) REVERT: Q 103 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8609 (p) REVERT: Q 291 LYS cc_start: 0.6412 (mttm) cc_final: 0.5684 (mmtt) REVERT: Q 372 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7530 (ptt90) REVERT: R 75 ILE cc_start: 0.8603 (pt) cc_final: 0.8342 (pt) REVERT: R 283 MET cc_start: 0.8714 (mmm) cc_final: 0.8017 (mmp) REVERT: R 286 ASP cc_start: 0.7720 (m-30) cc_final: 0.7312 (t0) REVERT: R 291 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8457 (mmtt) REVERT: R 352 PHE cc_start: 0.8657 (t80) cc_final: 0.8125 (t80) outliers start: 81 outliers final: 61 residues processed: 449 average time/residue: 1.1102 time to fit residues: 788.6135 Evaluate side-chains 443 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 372 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 194 THR 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 313 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 358 optimal weight: 2.9990 chunk 316 optimal weight: 0.5980 chunk 371 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS D 143 ASN E 156 HIS G 147 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096428 restraints weight = 178151.809| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.93 r_work: 0.3093 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39916 Z= 0.282 Angle : 0.580 7.116 54160 Z= 0.292 Chirality : 0.044 0.162 5990 Planarity : 0.004 0.050 6962 Dihedral : 8.493 151.551 5558 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.74 % Allowed : 11.93 % Favored : 86.33 % 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: -0.41 (0.12), residues: 4854 helix: -0.04 (0.12), residues: 2018 sheet: -0.85 (0.16), residues: 944 loop : 0.09 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 356 HIS 0.009 0.001 HIS E 156 PHE 0.015 0.001 PHE B 277 TYR 0.015 0.001 TYR B 255 ARG 0.006 0.000 ARG I 372 *********************** 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 452 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 379 time to evaluate : 5.818 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: A 130 GLU cc_start: 0.7899 (pm20) cc_final: 0.7448 (pm20) REVERT: A 137 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 188 ASP cc_start: 0.8745 (t70) cc_final: 0.7999 (t0) REVERT: A 276 HIS cc_start: 0.7859 (p90) cc_final: 0.7056 (p90) REVERT: A 363 MET cc_start: 0.8283 (mmp) cc_final: 0.7712 (mtp) REVERT: B 66 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8219 (tp40) REVERT: B 102 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7404 (ptpp) REVERT: B 295 ARG cc_start: 0.8126 (mtp180) cc_final: 0.7646 (ttm170) REVERT: C 55 ASP cc_start: 0.8458 (t0) cc_final: 0.7924 (m-30) REVERT: C 157 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7662 (p0) REVERT: D 117 ASN cc_start: 0.8605 (m-40) cc_final: 0.8067 (m110) REVERT: D 206 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7994 (mtm110) REVERT: D 247 GLU cc_start: 0.8579 (tp30) cc_final: 0.8304 (tp30) REVERT: E 94 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7215 (mtm-85) REVERT: F 74 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8810 (pt) REVERT: F 88 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7877 (ttt-90) REVERT: G 30 GLU cc_start: 0.8305 (mp0) cc_final: 0.7747 (tm-30) REVERT: G 88 ARG cc_start: 0.8016 (mmp80) cc_final: 0.7280 (mtp85) REVERT: G 124 SER cc_start: 0.8732 (t) cc_final: 0.8512 (m) REVERT: H 12 ASN cc_start: 0.8360 (m-40) cc_final: 0.8154 (m-40) REVERT: H 68 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7963 (mttm) REVERT: H 100 GLU cc_start: 0.7427 (tt0) cc_final: 0.7110 (tm-30) REVERT: I 125 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7256 (mt-10) REVERT: I 305 MET cc_start: 0.8793 (mmm) cc_final: 0.8579 (mmm) REVERT: I 355 MET cc_start: 0.7410 (mtt) cc_final: 0.7105 (mtt) REVERT: M 72 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: M 123 MET cc_start: 0.8793 (mmt) cc_final: 0.8450 (mmt) REVERT: M 167 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7611 (tm-30) REVERT: M 279 TYR cc_start: 0.8968 (t80) cc_final: 0.8598 (t80) REVERT: O 283 MET cc_start: 0.9004 (mmm) cc_final: 0.8751 (mmt) REVERT: O 287 ILE cc_start: 0.8929 (tt) cc_final: 0.8521 (mt) REVERT: P 313 MET cc_start: 0.8538 (mmm) cc_final: 0.8224 (mmm) REVERT: Q 44 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.7815 (mpt) REVERT: Q 47 MET cc_start: 0.8650 (mmm) cc_final: 0.7766 (ptt) REVERT: Q 103 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8664 (p) REVERT: Q 291 LYS cc_start: 0.6408 (mttm) cc_final: 0.5667 (mmtt) REVERT: Q 372 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7535 (ptt90) REVERT: R 75 ILE cc_start: 0.8610 (pt) cc_final: 0.8344 (pt) REVERT: R 283 MET cc_start: 0.8715 (mmm) cc_final: 0.8024 (mmp) REVERT: R 286 ASP cc_start: 0.7801 (m-30) cc_final: 0.7357 (t0) REVERT: R 291 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8459 (mmtt) REVERT: R 352 PHE cc_start: 0.8650 (t80) cc_final: 0.8116 (t80) outliers start: 73 outliers final: 59 residues processed: 436 average time/residue: 1.1388 time to fit residues: 788.3907 Evaluate side-chains 438 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 369 time to evaluate : 4.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 199 SER Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 194 THR 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 386 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 418 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 425 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 459 optimal weight: 2.9990 chunk 411 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 445 optimal weight: 3.9990 chunk 392 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 292 GLN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS N 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097387 restraints weight = 176318.732| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.85 r_work: 0.3127 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39916 Z= 0.169 Angle : 0.547 7.117 54160 Z= 0.272 Chirality : 0.042 0.149 5990 Planarity : 0.004 0.051 6962 Dihedral : 8.233 153.479 5556 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.48 % Allowed : 12.17 % Favored : 86.35 % 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: -0.18 (0.12), residues: 4854 helix: 0.15 (0.12), residues: 2021 sheet: -0.78 (0.16), residues: 946 loop : 0.23 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 356 HIS 0.008 0.001 HIS E 156 PHE 0.013 0.001 PHE B 277 TYR 0.015 0.001 TYR B 255 ARG 0.006 0.000 ARG P 28 *********************** 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 457 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 395 time to evaluate : 4.684 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: A 188 ASP cc_start: 0.8655 (t70) cc_final: 0.7897 (t0) REVERT: A 276 HIS cc_start: 0.7815 (p90) cc_final: 0.7070 (p90) REVERT: A 363 MET cc_start: 0.8326 (mmp) cc_final: 0.7824 (mtp) REVERT: B 66 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8182 (tp40) REVERT: B 102 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7365 (ptpp) REVERT: B 295 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7598 (ttm170) REVERT: C 55 ASP cc_start: 0.8353 (t0) cc_final: 0.7948 (m-30) REVERT: C 157 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7657 (p0) REVERT: D 106 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 117 ASN cc_start: 0.8553 (m-40) cc_final: 0.8098 (m-40) REVERT: D 206 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.7988 (mtm110) REVERT: D 247 GLU cc_start: 0.8555 (tp30) cc_final: 0.8218 (tt0) REVERT: D 279 TYR cc_start: 0.8960 (t80) cc_final: 0.8633 (t80) REVERT: E 94 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7212 (mtm-85) REVERT: F 74 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8775 (pt) REVERT: F 88 ARG cc_start: 0.8252 (ttt-90) cc_final: 0.7840 (ttt-90) REVERT: G 30 GLU cc_start: 0.8275 (mp0) cc_final: 0.7725 (tm-30) REVERT: G 88 ARG cc_start: 0.8072 (mmp80) cc_final: 0.7286 (mtp85) REVERT: G 124 SER cc_start: 0.8686 (t) cc_final: 0.8471 (m) REVERT: H 12 ASN cc_start: 0.8294 (m-40) cc_final: 0.8092 (m-40) REVERT: H 68 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7984 (mttm) REVERT: H 100 GLU cc_start: 0.7405 (tt0) cc_final: 0.7081 (tm-30) REVERT: H 132 MET cc_start: 0.8466 (ppp) cc_final: 0.8101 (tmm) REVERT: I 125 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7207 (mt-10) REVERT: I 305 MET cc_start: 0.8802 (mmm) cc_final: 0.8581 (mmm) REVERT: I 355 MET cc_start: 0.7424 (mtt) cc_final: 0.7116 (mtt) REVERT: M 72 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: M 123 MET cc_start: 0.8827 (mmt) cc_final: 0.8472 (mmt) REVERT: M 167 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7380 (tm-30) REVERT: M 207 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8433 (mm-30) REVERT: M 279 TYR cc_start: 0.8896 (t80) cc_final: 0.8537 (t80) REVERT: N 238 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8165 (ttmm) REVERT: O 283 MET cc_start: 0.8945 (mmm) cc_final: 0.8680 (mmt) REVERT: O 287 ILE cc_start: 0.8909 (tt) cc_final: 0.8525 (mt) REVERT: Q 44 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.7800 (mpt) REVERT: Q 47 MET cc_start: 0.8561 (mmm) cc_final: 0.7659 (ptt) REVERT: Q 54 VAL cc_start: 0.9593 (p) cc_final: 0.9295 (t) REVERT: Q 372 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7614 (ptt90) REVERT: R 283 MET cc_start: 0.8630 (mmm) cc_final: 0.7938 (mmp) REVERT: R 286 ASP cc_start: 0.7761 (m-30) cc_final: 0.7320 (t0) REVERT: R 291 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8475 (mmtt) REVERT: R 352 PHE cc_start: 0.8630 (t80) cc_final: 0.8127 (t80) outliers start: 62 outliers final: 47 residues processed: 440 average time/residue: 1.1444 time to fit residues: 793.2527 Evaluate side-chains 427 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 372 time to evaluate : 4.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 372 ARG 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 157 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 341 optimal weight: 5.9990 chunk 471 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 406 optimal weight: 0.0980 chunk 236 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN E 156 HIS G 38 GLN N 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098750 restraints weight = 176157.117| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.80 r_work: 0.3114 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39916 Z= 0.206 Angle : 0.553 7.219 54160 Z= 0.275 Chirality : 0.043 0.149 5990 Planarity : 0.004 0.050 6962 Dihedral : 8.190 153.492 5554 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.48 % Allowed : 12.43 % Favored : 86.09 % 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: -0.14 (0.12), residues: 4854 helix: 0.22 (0.12), residues: 2021 sheet: -0.82 (0.17), residues: 860 loop : 0.18 (0.15), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 356 HIS 0.009 0.001 HIS E 156 PHE 0.014 0.001 PHE B 277 TYR 0.014 0.001 TYR B 255 ARG 0.006 0.000 ARG I 372 ********************** 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 437 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 375 time to evaluate : 4.668 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: A 188 ASP cc_start: 0.8697 (t70) cc_final: 0.7923 (t0) REVERT: A 276 HIS cc_start: 0.7752 (p90) cc_final: 0.7017 (p90) REVERT: A 363 MET cc_start: 0.8335 (mmp) cc_final: 0.7831 (mtp) REVERT: B 66 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8178 (tp40) REVERT: B 102 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7377 (ptpp) REVERT: B 295 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7595 (ttm170) REVERT: C 55 ASP cc_start: 0.8355 (t0) cc_final: 0.7893 (m-30) REVERT: C 157 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7639 (p0) REVERT: D 106 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8626 (tm-30) REVERT: D 117 ASN cc_start: 0.8562 (m-40) cc_final: 0.8121 (m-40) REVERT: D 206 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7998 (mtm110) REVERT: D 247 GLU cc_start: 0.8471 (tp30) cc_final: 0.8226 (tp30) REVERT: D 279 TYR cc_start: 0.8934 (t80) cc_final: 0.8590 (t80) REVERT: E 94 ARG cc_start: 0.8085 (mtm110) cc_final: 0.7215 (mtm-85) REVERT: F 88 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7843 (ttt-90) REVERT: G 30 GLU cc_start: 0.8282 (mp0) cc_final: 0.7730 (tm-30) REVERT: G 88 ARG cc_start: 0.7963 (mmp80) cc_final: 0.7254 (mtp85) REVERT: G 124 SER cc_start: 0.8693 (t) cc_final: 0.8486 (m) REVERT: H 68 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7979 (mttm) REVERT: H 100 GLU cc_start: 0.7398 (tt0) cc_final: 0.7098 (tm-30) REVERT: H 132 MET cc_start: 0.8460 (ppp) cc_final: 0.8102 (tmm) REVERT: I 125 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7207 (mt-10) REVERT: I 305 MET cc_start: 0.8803 (mmm) cc_final: 0.8592 (mmm) REVERT: I 355 MET cc_start: 0.7428 (mtt) cc_final: 0.7211 (mtt) REVERT: M 72 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: M 123 MET cc_start: 0.8821 (mmt) cc_final: 0.8460 (mmt) REVERT: M 167 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7411 (tm-30) REVERT: M 279 TYR cc_start: 0.8922 (t80) cc_final: 0.8527 (t80) REVERT: N 238 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8163 (ttmm) REVERT: O 283 MET cc_start: 0.8951 (mmm) cc_final: 0.8688 (mmt) REVERT: O 287 ILE cc_start: 0.8897 (tt) cc_final: 0.8429 (mt) REVERT: P 132 MET cc_start: 0.8625 (ppp) cc_final: 0.8362 (ppp) REVERT: P 313 MET cc_start: 0.8490 (mmm) cc_final: 0.8170 (mmm) REVERT: Q 44 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.7763 (mpt) REVERT: Q 47 MET cc_start: 0.8602 (mmm) cc_final: 0.7779 (ptt) REVERT: Q 54 VAL cc_start: 0.9595 (p) cc_final: 0.9299 (t) REVERT: Q 372 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7567 (ptt90) REVERT: R 283 MET cc_start: 0.8633 (mmm) cc_final: 0.7948 (mmp) REVERT: R 286 ASP cc_start: 0.7764 (m-30) cc_final: 0.7322 (t0) REVERT: R 291 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8439 (mmtt) REVERT: R 352 PHE cc_start: 0.8529 (t80) cc_final: 0.8029 (t80) outliers start: 62 outliers final: 51 residues processed: 421 average time/residue: 1.0856 time to fit residues: 721.0825 Evaluate side-chains 429 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 371 time to evaluate : 4.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 257 CYS Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 148 THR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain P residue 344 SER Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 372 ARG 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 85 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 474 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN E 156 HIS M 297 ASN N 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099076 restraints weight = 177231.598| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.89 r_work: 0.3105 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39916 Z= 0.225 Angle : 0.558 7.783 54160 Z= 0.278 Chirality : 0.043 0.150 5990 Planarity : 0.004 0.050 6962 Dihedral : 8.155 152.817 5554 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.55 % Allowed : 12.43 % Favored : 86.02 % 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: -0.12 (0.12), residues: 4854 helix: 0.26 (0.12), residues: 2020 sheet: -0.84 (0.17), residues: 866 loop : 0.18 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 356 HIS 0.009 0.001 HIS E 156 PHE 0.014 0.001 PHE B 277 TYR 0.014 0.001 TYR B 255 ARG 0.006 0.000 ARG P 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32165.26 seconds wall clock time: 551 minutes 28.75 seconds (33088.75 seconds total)