Starting phenix.real_space_refine on Mon Sep 30 07:11:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/09_2024/8uxx_42788_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/09_2024/8uxx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/09_2024/8uxx_42788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/09_2024/8uxx_42788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/09_2024/8uxx_42788_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxx_42788/09_2024/8uxx_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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 28.54, per 1000 atoms: 0.37 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: 24.05 Conformation dependent library (CDL) restraints added in 8.3 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: 5.89 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: 32.22 Time building geometry restraints manager: 27.79 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: 1.600 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: 1.090 Extract box with map and model: 2.160 Check model and map are aligned: 0.450 Set scattering table: 0.550 Process input model: 146.010 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.190 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.060 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 96 poor density : 747 time to evaluate : 4.999 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: 1.1950 time to fit residues: 1502.3436 Evaluate side-chains 537 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 489 time to evaluate : 4.618 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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 fitting. rotamer outliers: 78 poor density : 509 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.7697 (t0) cc_final: 0.6907 (t0) REVERT: A 146 MET cc_start: 0.8440 (mmm) cc_final: 0.8132 (mmm) REVERT: A 160 GLN cc_start: 0.6845 (pt0) cc_final: 0.6025 (pt0) REVERT: A 183 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 276 HIS cc_start: 0.7540 (p90) cc_final: 0.7114 (p90) REVERT: A 341 ASN cc_start: 0.7830 (t0) cc_final: 0.6618 (t0) REVERT: B 21 LYS cc_start: 0.8549 (mtmt) cc_final: 0.7837 (mmmt) REVERT: B 51 ASP cc_start: 0.8190 (m-30) cc_final: 0.7683 (t0) REVERT: B 224 GLU cc_start: 0.7661 (pt0) cc_final: 0.7258 (mt-10) REVERT: B 237 MET cc_start: 0.8697 (mmm) cc_final: 0.8452 (mmm) REVERT: B 249 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7891 (mttm) REVERT: B 255 TYR cc_start: 0.8546 (p90) cc_final: 0.8141 (p90) REVERT: B 294 TYR cc_start: 0.8752 (m-80) cc_final: 0.8514 (m-80) REVERT: B 295 ARG cc_start: 0.7442 (mtp180) cc_final: 0.7163 (ttp80) REVERT: B 305 MET cc_start: 0.9049 (mmm) cc_final: 0.8846 (mmt) REVERT: C 55 ASP cc_start: 0.7727 (t0) cc_final: 0.7196 (m-30) REVERT: C 157 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7018 (p0) REVERT: C 183 LYS cc_start: 0.8289 (mmtt) cc_final: 0.8039 (mmmm) REVERT: C 327 MET cc_start: 0.7572 (tpp) cc_final: 0.7105 (tpt) REVERT: C 347 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8611 (pt) REVERT: D 1 MET cc_start: 0.8689 (ptt) cc_final: 0.8456 (ptt) REVERT: D 103 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7413 (mt-10) REVERT: D 106 GLN cc_start: 0.7678 (pt0) cc_final: 0.7356 (tm-30) REVERT: D 113 MET cc_start: 0.8258 (tpp) cc_final: 0.7410 (mmt) REVERT: D 117 ASN cc_start: 0.8100 (m-40) cc_final: 0.7821 (m-40) REVERT: D 157 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7037 (mpp) REVERT: D 206 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7541 (mtt90) REVERT: D 230 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7290 (pt0) REVERT: D 247 GLU cc_start: 0.7972 (tp30) cc_final: 0.7590 (tp30) REVERT: D 286 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7209 (tptt) REVERT: E 59 ASN cc_start: 0.8319 (t0) cc_final: 0.8092 (t0) REVERT: E 79 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6883 (mt-10) REVERT: E 94 ARG cc_start: 0.7706 (mtp-110) cc_final: 0.7206 (mtm-85) REVERT: E 156 HIS cc_start: 0.7702 (t-90) cc_final: 0.7157 (t-90) REVERT: E 166 LYS cc_start: 0.7488 (mtpm) cc_final: 0.7286 (mmtt) REVERT: E 170 MET cc_start: 0.8396 (mmt) cc_final: 0.7992 (mmt) REVERT: F 77 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8272 (ttpt) REVERT: G 19 GLN cc_start: 0.7893 (pm20) cc_final: 0.7685 (pp30) REVERT: G 20 ASP cc_start: 0.8044 (m-30) cc_final: 0.7792 (m-30) REVERT: G 30 GLU cc_start: 0.8240 (mp0) cc_final: 0.7553 (tm-30) REVERT: G 82 ASP cc_start: 0.7303 (m-30) cc_final: 0.7090 (m-30) REVERT: G 88 ARG cc_start: 0.7494 (mmp80) cc_final: 0.6803 (mtm110) REVERT: G 124 SER cc_start: 0.7833 (t) cc_final: 0.7430 (m) REVERT: G 132 LYS cc_start: 0.8121 (mttm) cc_final: 0.7907 (mmtt) REVERT: H 68 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7476 (mttp) REVERT: H 100 GLU cc_start: 0.7274 (tt0) cc_final: 0.6727 (tm-30) REVERT: H 107 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7097 (tm-30) REVERT: H 119 MET cc_start: 0.7978 (ttm) cc_final: 0.7746 (ttp) REVERT: H 169 TYR cc_start: 0.8152 (m-80) cc_final: 0.7850 (m-10) REVERT: H 194 THR cc_start: 0.8760 (t) cc_final: 0.8464 (p) REVERT: I 44 MET cc_start: 0.8450 (mtp) cc_final: 0.8198 (mtm) REVERT: I 132 MET cc_start: 0.7637 (pmm) cc_final: 0.7289 (pmm) REVERT: I 194 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8449 (p) REVERT: I 280 ASN cc_start: 0.8004 (m-40) cc_final: 0.7746 (m-40) REVERT: I 283 MET cc_start: 0.8410 (tpp) cc_final: 0.7883 (tpp) REVERT: M 90 PHE cc_start: 0.8229 (m-80) cc_final: 0.7591 (m-80) REVERT: M 167 GLU cc_start: 0.7565 (mt-10) cc_final: 0.6825 (tm-30) REVERT: N 54 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7872 (m) REVERT: N 270 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7925 (tt0) REVERT: O 57 GLU cc_start: 0.7518 (tt0) cc_final: 0.7152 (tp30) REVERT: O 81 ASP cc_start: 0.8524 (m-30) cc_final: 0.8289 (m-30) REVERT: O 82 MET cc_start: 0.8707 (tpt) cc_final: 0.8472 (tpt) REVERT: O 118 LYS cc_start: 0.7631 (mttm) cc_final: 0.7182 (mtpp) REVERT: O 210 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7407 (ttp80) REVERT: O 222 ASP cc_start: 0.8020 (t0) cc_final: 0.7626 (p0) REVERT: O 283 MET cc_start: 0.8912 (mmm) cc_final: 0.8434 (mmt) REVERT: O 287 ILE cc_start: 0.8391 (tt) cc_final: 0.8075 (mt) REVERT: O 292 ASP cc_start: 0.8540 (m-30) cc_final: 0.8213 (m-30) REVERT: O 305 MET cc_start: 0.8669 (mmm) cc_final: 0.8303 (mmm) REVERT: O 325 MET cc_start: 0.8003 (ptm) cc_final: 0.7563 (ptm) REVERT: P 47 MET cc_start: 0.3618 (mmm) cc_final: 0.3403 (mmt) REVERT: P 72 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7058 (tt0) REVERT: P 82 MET cc_start: 0.9100 (tpt) cc_final: 0.8820 (tpt) REVERT: P 119 MET cc_start: 0.7881 (ttp) cc_final: 0.7464 (ttp) REVERT: P 227 MET cc_start: 0.8552 (mmm) cc_final: 0.8219 (mmm) REVERT: P 326 LYS cc_start: 0.7944 (pttp) cc_final: 0.7670 (ptmm) REVERT: Q 44 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.7729 (mpt) REVERT: Q 47 MET cc_start: 0.8404 (mmm) cc_final: 0.7269 (ptt) REVERT: Q 54 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9173 (t) REVERT: Q 81 ASP cc_start: 0.8657 (m-30) cc_final: 0.8399 (m-30) REVERT: Q 103 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8157 (p) REVERT: Q 105 LEU cc_start: 0.8193 (mt) cc_final: 0.7922 (mt) REVERT: Q 269 MET cc_start: 0.8715 (ptm) cc_final: 0.8381 (ptm) REVERT: Q 277 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8327 (t) REVERT: Q 291 LYS cc_start: 0.6061 (mttm) cc_final: 0.5600 (mmtt) REVERT: Q 326 LYS cc_start: 0.7909 (pttt) cc_final: 0.7537 (mmtm) REVERT: Q 328 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7444 (ttmm) REVERT: R 82 MET cc_start: 0.8476 (mmm) cc_final: 0.7500 (tpt) REVERT: R 175 ILE cc_start: 0.8698 (mt) cc_final: 0.8418 (mt) REVERT: R 286 ASP cc_start: 0.7566 (m-30) cc_final: 0.7078 (t0) REVERT: R 291 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8027 (mmtt) REVERT: R 352 PHE cc_start: 0.8616 (t80) cc_final: 0.8083 (t80) outliers start: 78 outliers final: 41 residues processed: 564 average time/residue: 1.1928 time to fit residues: 1054.9472 Evaluate side-chains 469 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 416 time to evaluate : 4.584 ------------------------------------------------------------------------------- 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 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 161 TYR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 286 LYS 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 246 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 369 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 444 optimal weight: 4.9990 chunk 480 optimal weight: 4.9990 chunk 396 optimal weight: 0.9990 chunk 441 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 140 HIS C 196 ASN D 160 HIS D 292 GLN E 40 GLN E 115 ASN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 39916 Z= 0.436 Angle : 0.700 8.250 54160 Z= 0.366 Chirality : 0.048 0.221 5990 Planarity : 0.005 0.057 6962 Dihedral : 10.054 171.555 5588 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.00 % Allowed : 9.67 % Favored : 88.33 % 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: -1.13 (0.12), residues: 4854 helix: -0.94 (0.11), residues: 2000 sheet: -1.03 (0.17), residues: 892 loop : -0.09 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 356 HIS 0.008 0.001 HIS A 404 PHE 0.023 0.002 PHE B 277 TYR 0.019 0.002 TYR B 88 ARG 0.007 0.001 ARG D 162 *********************** 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 511 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 427 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: A 148 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7600 (mt-10) REVERT: A 262 PRO cc_start: 0.8469 (Cg_endo) cc_final: 0.8219 (Cg_exo) REVERT: A 276 HIS cc_start: 0.7446 (p90) cc_final: 0.7190 (p90) REVERT: A 406 LYS cc_start: 0.8247 (pttp) cc_final: 0.7933 (ttpp) REVERT: B 6 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6962 (mt) REVERT: B 21 LYS cc_start: 0.8554 (mtmt) cc_final: 0.7770 (mmmt) REVERT: B 51 ASP cc_start: 0.8236 (m-30) cc_final: 0.7458 (t0) REVERT: B 72 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6679 (tt0) REVERT: B 224 GLU cc_start: 0.7630 (pt0) cc_final: 0.7233 (mt-10) REVERT: B 237 MET cc_start: 0.8756 (mmm) cc_final: 0.8499 (mmm) REVERT: B 249 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7886 (mttm) REVERT: B 255 TYR cc_start: 0.8682 (p90) cc_final: 0.8262 (p90) REVERT: B 295 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7060 (ttm170) REVERT: B 361 MET cc_start: 0.8269 (ptp) cc_final: 0.7795 (ptm) REVERT: B 365 ASP cc_start: 0.8215 (t0) cc_final: 0.7980 (m-30) REVERT: C 55 ASP cc_start: 0.7934 (t0) cc_final: 0.7313 (m-30) REVERT: C 157 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7137 (p0) REVERT: C 178 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7913 (ttm-80) REVERT: C 183 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8019 (mmmm) REVERT: C 327 MET cc_start: 0.7652 (tpp) cc_final: 0.7051 (tpt) REVERT: D 1 MET cc_start: 0.8634 (ptt) cc_final: 0.8401 (ptt) REVERT: D 105 GLU cc_start: 0.7121 (tt0) cc_final: 0.6844 (tm-30) REVERT: D 117 ASN cc_start: 0.8300 (m-40) cc_final: 0.7830 (m-40) REVERT: D 206 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7448 (mtt90) REVERT: D 230 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7312 (pt0) REVERT: E 79 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6920 (mt-10) REVERT: E 94 ARG cc_start: 0.7529 (mtp-110) cc_final: 0.7078 (mtm-85) REVERT: E 156 HIS cc_start: 0.7651 (t-90) cc_final: 0.7357 (t-90) REVERT: E 166 LYS cc_start: 0.7667 (mtpm) cc_final: 0.7369 (mmtt) REVERT: F 88 ARG cc_start: 0.7646 (ttt-90) cc_final: 0.7211 (ttt-90) REVERT: G 20 ASP cc_start: 0.8124 (m-30) cc_final: 0.7869 (m-30) REVERT: G 30 GLU cc_start: 0.8232 (mp0) cc_final: 0.7612 (tm-30) REVERT: G 88 ARG cc_start: 0.7495 (mmp80) cc_final: 0.6805 (mtm110) REVERT: G 124 SER cc_start: 0.7826 (t) cc_final: 0.7453 (m) REVERT: G 132 LYS cc_start: 0.8079 (mttm) cc_final: 0.7763 (mmmt) REVERT: H 68 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7434 (mttp) REVERT: H 100 GLU cc_start: 0.7233 (tt0) cc_final: 0.6642 (tm-30) REVERT: I 125 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7182 (mt-10) REVERT: I 280 ASN cc_start: 0.8096 (m-40) cc_final: 0.7851 (m-40) REVERT: M 90 PHE cc_start: 0.8194 (m-80) cc_final: 0.7596 (m-80) REVERT: M 167 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7279 (tm-30) REVERT: M 207 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8185 (mm-30) REVERT: M 211 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: M 287 ILE cc_start: 0.8134 (tp) cc_final: 0.7844 (tt) REVERT: M 299 MET cc_start: 0.8565 (mtm) cc_final: 0.8327 (mtm) REVERT: N 54 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7963 (m) REVERT: N 270 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7798 (tt0) REVERT: O 57 GLU cc_start: 0.7524 (tt0) cc_final: 0.7060 (tp30) REVERT: O 118 LYS cc_start: 0.7665 (mttm) cc_final: 0.7206 (mtpp) REVERT: O 222 ASP cc_start: 0.8069 (t0) cc_final: 0.7611 (p0) REVERT: O 283 MET cc_start: 0.8842 (mmm) cc_final: 0.8433 (mmt) REVERT: O 287 ILE cc_start: 0.8467 (tt) cc_final: 0.8107 (mt) REVERT: O 292 ASP cc_start: 0.8636 (m-30) cc_final: 0.8232 (m-30) REVERT: O 305 MET cc_start: 0.8419 (mmm) cc_final: 0.8029 (mmt) REVERT: O 325 MET cc_start: 0.8008 (ptm) cc_final: 0.7540 (ptm) REVERT: P 72 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7179 (tt0) REVERT: P 82 MET cc_start: 0.9102 (tpt) cc_final: 0.8859 (tpt) REVERT: P 176 MET cc_start: 0.8693 (mmp) cc_final: 0.8367 (mmm) REVERT: P 227 MET cc_start: 0.8380 (mmm) cc_final: 0.8105 (mmm) REVERT: P 326 LYS cc_start: 0.8187 (pttp) cc_final: 0.7881 (ptmm) REVERT: Q 44 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.7635 (mpt) REVERT: Q 47 MET cc_start: 0.8431 (mmm) cc_final: 0.7323 (ptt) REVERT: Q 54 VAL cc_start: 0.9440 (OUTLIER) cc_final: 0.9174 (t) REVERT: Q 105 LEU cc_start: 0.8438 (mt) cc_final: 0.8146 (mt) REVERT: Q 177 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8566 (tmt170) REVERT: Q 269 MET cc_start: 0.8919 (ptm) cc_final: 0.8656 (ptm) REVERT: Q 291 LYS cc_start: 0.6063 (mttm) cc_final: 0.5396 (mmtt) REVERT: Q 326 LYS cc_start: 0.7956 (pttt) cc_final: 0.7670 (mmtm) REVERT: Q 328 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7810 (ttmm) REVERT: R 283 MET cc_start: 0.8562 (mmm) cc_final: 0.7787 (mmp) REVERT: R 286 ASP cc_start: 0.7468 (m-30) cc_final: 0.6991 (t0) REVERT: R 291 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8037 (mmtt) REVERT: R 352 PHE cc_start: 0.8600 (t80) cc_final: 0.8032 (t80) REVERT: R 358 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8413 (p) outliers start: 84 outliers final: 55 residues processed: 492 average time/residue: 1.1188 time to fit residues: 866.7358 Evaluate side-chains 461 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 397 time to evaluate : 4.583 ------------------------------------------------------------------------------- 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 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 116 ARG Chi-restraints excluded: chain D residue 161 TYR 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 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 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 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 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 Chi-restraints excluded: chain R residue 358 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 2.9990 chunk 334 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 446 optimal weight: 3.9990 chunk 472 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 423 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** Q 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39916 Z= 0.214 Angle : 0.604 7.934 54160 Z= 0.308 Chirality : 0.044 0.182 5990 Planarity : 0.004 0.051 6962 Dihedral : 9.455 174.287 5580 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.72 % Allowed : 10.41 % Favored : 87.88 % 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: -0.79 (0.12), residues: 4854 helix: -0.55 (0.11), residues: 2001 sheet: -1.05 (0.17), residues: 860 loop : 0.06 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 356 HIS 0.006 0.001 HIS A 404 PHE 0.018 0.001 PHE B 277 TYR 0.015 0.001 TYR B 88 ARG 0.005 0.000 ARG I 372 *********************** 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 492 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 420 time to evaluate : 4.665 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: 0.6988 (pm20) cc_final: 0.6623 (pm20) REVERT: A 148 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 188 ASP cc_start: 0.7576 (t0) cc_final: 0.6654 (t0) REVERT: A 276 HIS cc_start: 0.7732 (p90) cc_final: 0.6999 (p90) REVERT: A 406 LYS cc_start: 0.8193 (pttp) cc_final: 0.7960 (ttpp) REVERT: A 410 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7178 (mt-10) REVERT: B 6 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7038 (mt) REVERT: B 51 ASP cc_start: 0.8217 (m-30) cc_final: 0.7498 (t0) REVERT: B 72 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6349 (tt0) REVERT: B 224 GLU cc_start: 0.7538 (pt0) cc_final: 0.7221 (mt-10) REVERT: B 249 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7831 (mtpp) REVERT: B 255 TYR cc_start: 0.8680 (p90) cc_final: 0.8320 (p90) REVERT: B 295 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7005 (ttm170) REVERT: B 361 MET cc_start: 0.8086 (ptp) cc_final: 0.7688 (ptm) REVERT: B 365 ASP cc_start: 0.8189 (t0) cc_final: 0.7973 (m-30) REVERT: C 55 ASP cc_start: 0.7965 (t0) cc_final: 0.7299 (m-30) REVERT: C 157 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7125 (p0) REVERT: C 183 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7979 (mmmm) REVERT: D 1 MET cc_start: 0.8586 (ptt) cc_final: 0.8354 (ptt) REVERT: D 105 GLU cc_start: 0.6887 (tt0) cc_final: 0.6674 (tm-30) REVERT: D 117 ASN cc_start: 0.8296 (m-40) cc_final: 0.7797 (m-40) REVERT: D 206 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7523 (mtt90) REVERT: D 230 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7305 (pt0) REVERT: D 247 GLU cc_start: 0.8082 (tp30) cc_final: 0.7688 (tp30) REVERT: E 79 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6911 (mt-10) REVERT: E 94 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7066 (mtm-85) REVERT: E 166 LYS cc_start: 0.7684 (mtpm) cc_final: 0.7379 (mmtt) REVERT: F 88 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.7151 (ttt-90) REVERT: G 17 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7378 (m) REVERT: G 30 GLU cc_start: 0.8215 (mp0) cc_final: 0.7614 (tm-30) REVERT: G 88 ARG cc_start: 0.7528 (mmp80) cc_final: 0.6736 (mtm110) REVERT: G 124 SER cc_start: 0.7742 (t) cc_final: 0.7377 (m) REVERT: G 132 LYS cc_start: 0.7950 (mttm) cc_final: 0.7682 (mmmt) REVERT: H 47 MET cc_start: 0.6239 (mmt) cc_final: 0.5946 (mmt) REVERT: H 68 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7438 (mttp) REVERT: H 100 GLU cc_start: 0.7207 (tt0) cc_final: 0.6639 (tm-30) REVERT: H 194 THR cc_start: 0.8788 (t) cc_final: 0.8532 (p) REVERT: H 305 MET cc_start: 0.9037 (tpt) cc_final: 0.8743 (tpt) REVERT: I 125 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7171 (mt-10) REVERT: I 194 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8392 (p) REVERT: M 90 PHE cc_start: 0.8098 (m-80) cc_final: 0.7673 (m-80) REVERT: M 167 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7070 (tm-30) REVERT: M 207 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8118 (mm-30) REVERT: M 279 TYR cc_start: 0.8778 (t80) cc_final: 0.8453 (t80) REVERT: N 54 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7973 (m) REVERT: O 57 GLU cc_start: 0.7465 (tt0) cc_final: 0.7095 (tp30) REVERT: O 118 LYS cc_start: 0.7632 (mttm) cc_final: 0.7157 (mtpp) REVERT: O 222 ASP cc_start: 0.8072 (t0) cc_final: 0.7771 (p0) REVERT: O 283 MET cc_start: 0.8794 (mmm) cc_final: 0.8373 (mmt) REVERT: O 287 ILE cc_start: 0.8437 (tt) cc_final: 0.8083 (mt) REVERT: P 72 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7082 (tt0) REVERT: P 82 MET cc_start: 0.9069 (tpt) cc_final: 0.8836 (tpt) REVERT: P 165 ILE cc_start: 0.8738 (mt) cc_final: 0.8531 (mt) REVERT: P 176 MET cc_start: 0.8655 (mmp) cc_final: 0.8314 (mmm) REVERT: P 326 LYS cc_start: 0.8159 (pttp) cc_final: 0.7941 (ptmm) REVERT: Q 44 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.7603 (mpt) REVERT: Q 47 MET cc_start: 0.8372 (mmm) cc_final: 0.7377 (ptt) REVERT: Q 54 VAL cc_start: 0.9411 (p) cc_final: 0.9184 (t) REVERT: Q 105 LEU cc_start: 0.8408 (mt) cc_final: 0.8141 (mt) REVERT: Q 177 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8464 (ttt180) REVERT: Q 269 MET cc_start: 0.8909 (ptm) cc_final: 0.8682 (ptm) REVERT: Q 291 LYS cc_start: 0.5933 (mttm) cc_final: 0.5639 (mmtt) REVERT: Q 326 LYS cc_start: 0.7906 (pttt) cc_final: 0.7587 (mmtm) REVERT: Q 328 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7743 (ttmm) REVERT: R 283 MET cc_start: 0.8435 (mmm) cc_final: 0.7691 (mmp) REVERT: R 286 ASP cc_start: 0.7434 (m-30) cc_final: 0.6957 (t0) REVERT: R 291 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8038 (mmtt) REVERT: R 352 PHE cc_start: 0.8541 (t80) cc_final: 0.7985 (t80) outliers start: 72 outliers final: 51 residues processed: 471 average time/residue: 1.1821 time to fit residues: 889.1450 Evaluate side-chains 455 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 396 time to evaluate : 4.645 ------------------------------------------------------------------------------- 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 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 39 GLU 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 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 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 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 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 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 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 177 ARG Chi-restraints excluded: chain Q residue 277 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 403 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 424 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN H 87 HIS M 162 ASN M 314 GLN N 162 ASN Q 162 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39916 Z= 0.241 Angle : 0.583 6.996 54160 Z= 0.294 Chirality : 0.043 0.170 5990 Planarity : 0.004 0.051 6962 Dihedral : 8.921 155.425 5569 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.69 % Allowed : 10.98 % Favored : 87.33 % 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: -0.59 (0.12), residues: 4854 helix: -0.28 (0.12), residues: 2006 sheet: -0.98 (0.16), residues: 956 loop : 0.12 (0.15), residues: 1892 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 0.018 0.001 PHE B 277 TYR 0.013 0.001 TYR B 88 ARG 0.006 0.000 ARG D 116 *********************** 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 480 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 409 time to evaluate : 4.662 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: 0.6908 (pm20) cc_final: 0.6583 (pm20) REVERT: A 276 HIS cc_start: 0.7751 (p90) cc_final: 0.7057 (p90) REVERT: A 363 MET cc_start: 0.7689 (mmm) cc_final: 0.7156 (mtp) REVERT: A 406 LYS cc_start: 0.8165 (pttp) cc_final: 0.7958 (ttpp) REVERT: B 51 ASP cc_start: 0.8176 (m-30) cc_final: 0.7460 (t0) REVERT: B 72 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6442 (tt0) REVERT: B 102 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6780 (ptpp) REVERT: B 224 GLU cc_start: 0.7464 (pt0) cc_final: 0.7196 (mt-10) REVERT: B 249 LYS cc_start: 0.8498 (mtmt) cc_final: 0.7855 (mtpp) REVERT: B 295 ARG cc_start: 0.7466 (mtp180) cc_final: 0.7019 (ttm170) REVERT: B 361 MET cc_start: 0.8051 (ptp) cc_final: 0.7680 (ptm) REVERT: B 365 ASP cc_start: 0.8188 (t0) cc_final: 0.7910 (m-30) REVERT: C 55 ASP cc_start: 0.8027 (t0) cc_final: 0.7367 (m-30) REVERT: C 157 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7128 (p0) REVERT: C 183 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7887 (mmmm) REVERT: D 1 MET cc_start: 0.8707 (ptt) cc_final: 0.8439 (ptt) REVERT: D 117 ASN cc_start: 0.8452 (m-40) cc_final: 0.7784 (m110) REVERT: D 206 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7310 (mtm110) REVERT: D 230 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7327 (pt0) REVERT: D 247 GLU cc_start: 0.8081 (tp30) cc_final: 0.7670 (tp30) REVERT: D 279 TYR cc_start: 0.8308 (t80) cc_final: 0.8069 (t80) REVERT: E 79 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6915 (mt-10) REVERT: E 94 ARG cc_start: 0.7648 (mtp-110) cc_final: 0.7418 (mtm110) REVERT: E 166 LYS cc_start: 0.7723 (mtpm) cc_final: 0.7395 (mmtt) REVERT: F 88 ARG cc_start: 0.7454 (ttt-90) cc_final: 0.7079 (ttt-90) REVERT: G 30 GLU cc_start: 0.8222 (mp0) cc_final: 0.7622 (tm-30) REVERT: G 88 ARG cc_start: 0.7509 (mmp80) cc_final: 0.6610 (mtm110) REVERT: G 124 SER cc_start: 0.7760 (t) cc_final: 0.7410 (m) REVERT: G 132 LYS cc_start: 0.7934 (mttm) cc_final: 0.7681 (mmmt) REVERT: H 68 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7266 (mttm) REVERT: H 100 GLU cc_start: 0.7206 (tt0) cc_final: 0.6781 (tm-30) REVERT: H 194 THR cc_start: 0.8832 (t) cc_final: 0.8556 (p) REVERT: I 125 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7157 (mt-10) REVERT: M 90 PHE cc_start: 0.8010 (m-80) cc_final: 0.7701 (m-80) REVERT: M 123 MET cc_start: 0.8852 (mmt) cc_final: 0.8381 (mmt) REVERT: M 167 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7071 (tm-30) REVERT: M 207 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8163 (mm-30) REVERT: M 279 TYR cc_start: 0.8774 (t80) cc_final: 0.8413 (t80) REVERT: N 54 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7985 (m) REVERT: O 57 GLU cc_start: 0.7410 (tt0) cc_final: 0.7071 (tp30) REVERT: O 118 LYS cc_start: 0.7642 (mttm) cc_final: 0.7165 (mtpp) REVERT: O 222 ASP cc_start: 0.8050 (t0) cc_final: 0.7536 (p0) REVERT: O 283 MET cc_start: 0.8782 (mmm) cc_final: 0.8397 (mmt) REVERT: O 287 ILE cc_start: 0.8613 (tt) cc_final: 0.8107 (mt) REVERT: P 72 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7069 (tt0) REVERT: P 176 MET cc_start: 0.8665 (mmp) cc_final: 0.8359 (mmm) REVERT: P 326 LYS cc_start: 0.8183 (pttp) cc_final: 0.7915 (ptmm) REVERT: Q 44 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.7495 (mpt) REVERT: Q 47 MET cc_start: 0.8317 (mmm) cc_final: 0.7373 (ptt) REVERT: Q 54 VAL cc_start: 0.9413 (p) cc_final: 0.9188 (t) REVERT: Q 103 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8128 (p) REVERT: Q 105 LEU cc_start: 0.8468 (mt) cc_final: 0.8169 (mt) REVERT: Q 269 MET cc_start: 0.8850 (ptm) cc_final: 0.8593 (ptm) REVERT: Q 291 LYS cc_start: 0.5937 (mttm) cc_final: 0.5382 (mmtt) REVERT: Q 326 LYS cc_start: 0.7900 (pttt) cc_final: 0.7534 (mmtm) REVERT: Q 328 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7424 (tptt) REVERT: Q 372 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7228 (ptt90) REVERT: R 283 MET cc_start: 0.8359 (mmm) cc_final: 0.7621 (mmp) REVERT: R 286 ASP cc_start: 0.7390 (m-30) cc_final: 0.6929 (t0) REVERT: R 291 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8055 (mmtt) REVERT: R 352 PHE cc_start: 0.8513 (t80) cc_final: 0.7935 (t80) outliers start: 71 outliers final: 48 residues processed: 464 average time/residue: 1.1422 time to fit residues: 841.5185 Evaluate side-chains 447 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 392 time to evaluate : 4.646 ------------------------------------------------------------------------------- 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 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 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 221 ASP 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 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 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 372 ARG 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 159 optimal weight: 0.8980 chunk 425 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 277 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 473 optimal weight: 2.9990 chunk 392 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 E 156 HIS M 161 HIS N 162 ASN Q 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 39916 Z= 0.373 Angle : 0.623 7.328 54160 Z= 0.317 Chirality : 0.045 0.188 5990 Planarity : 0.004 0.049 6962 Dihedral : 8.815 150.907 5561 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.93 % Allowed : 11.43 % Favored : 86.64 % 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: -0.69 (0.12), residues: 4854 helix: -0.30 (0.12), residues: 2013 sheet: -1.13 (0.17), residues: 869 loop : -0.02 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 102 HIS 0.010 0.001 HIS E 156 PHE 0.019 0.002 PHE B 277 TYR 0.023 0.001 TYR B 255 ARG 0.005 0.000 ARG D 116 *********************** 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 481 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 400 time to evaluate : 4.703 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: 0.6951 (pm20) cc_final: 0.6552 (pm20) REVERT: A 137 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: A 188 ASP cc_start: 0.7445 (t0) cc_final: 0.7069 (t0) REVERT: A 276 HIS cc_start: 0.7701 (p90) cc_final: 0.6961 (p90) REVERT: A 363 MET cc_start: 0.7691 (mmm) cc_final: 0.7200 (mtp) REVERT: B 6 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7014 (mt) REVERT: B 51 ASP cc_start: 0.8038 (m-30) cc_final: 0.7403 (t0) REVERT: B 66 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7264 (tp40) REVERT: B 72 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6482 (tt0) REVERT: B 102 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6902 (ptpp) REVERT: B 224 GLU cc_start: 0.7472 (pt0) cc_final: 0.7193 (mt-10) REVERT: B 249 LYS cc_start: 0.8617 (mtmt) cc_final: 0.7960 (mtpp) REVERT: B 295 ARG cc_start: 0.7517 (mtp180) cc_final: 0.7008 (ttm170) REVERT: B 361 MET cc_start: 0.8094 (ptp) cc_final: 0.7718 (ptm) REVERT: B 365 ASP cc_start: 0.8190 (t0) cc_final: 0.7917 (m-30) REVERT: C 55 ASP cc_start: 0.8027 (t0) cc_final: 0.7318 (m-30) REVERT: C 157 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7132 (p0) REVERT: C 183 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7858 (mmmm) REVERT: C 251 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: D 1 MET cc_start: 0.8745 (ptt) cc_final: 0.8464 (ptt) REVERT: D 105 GLU cc_start: 0.7080 (tt0) cc_final: 0.6835 (tm-30) REVERT: D 117 ASN cc_start: 0.8533 (m-40) cc_final: 0.7897 (m110) REVERT: D 206 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7361 (mtm110) REVERT: D 230 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7365 (pt0) REVERT: D 247 GLU cc_start: 0.8057 (tp30) cc_final: 0.7656 (tp30) REVERT: D 306 ARG cc_start: 0.5678 (mtt90) cc_final: 0.5423 (mtt90) REVERT: E 79 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6937 (mt-10) REVERT: E 94 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7420 (mtm110) REVERT: E 166 LYS cc_start: 0.7806 (mtpm) cc_final: 0.7466 (mmtt) REVERT: F 74 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8162 (pt) REVERT: F 88 ARG cc_start: 0.7608 (ttt-90) cc_final: 0.7237 (ttt-90) REVERT: G 30 GLU cc_start: 0.8241 (mp0) cc_final: 0.7662 (tm-30) REVERT: G 38 GLN cc_start: 0.8443 (tp40) cc_final: 0.8238 (tp40) REVERT: G 88 ARG cc_start: 0.7555 (mmp80) cc_final: 0.6693 (mtm110) REVERT: G 124 SER cc_start: 0.7792 (t) cc_final: 0.7455 (m) REVERT: G 132 LYS cc_start: 0.7931 (mttm) cc_final: 0.7692 (mmmt) REVERT: H 12 ASN cc_start: 0.7968 (m-40) cc_final: 0.7713 (m-40) REVERT: H 68 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7333 (mttm) REVERT: H 100 GLU cc_start: 0.7230 (tt0) cc_final: 0.6810 (tm-30) REVERT: I 125 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7126 (mt-10) REVERT: M 90 PHE cc_start: 0.8094 (m-80) cc_final: 0.7780 (m-80) REVERT: M 123 MET cc_start: 0.8779 (mmt) cc_final: 0.8411 (mmt) REVERT: M 167 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7284 (tm-30) REVERT: M 207 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8112 (mm-30) REVERT: N 54 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8068 (m) REVERT: O 57 GLU cc_start: 0.7448 (tt0) cc_final: 0.7083 (tp30) REVERT: O 222 ASP cc_start: 0.8065 (t0) cc_final: 0.7515 (p0) REVERT: O 283 MET cc_start: 0.8787 (mmm) cc_final: 0.8406 (mmt) REVERT: O 287 ILE cc_start: 0.8744 (tt) cc_final: 0.8238 (mt) REVERT: O 325 MET cc_start: 0.7801 (ptm) cc_final: 0.7370 (ptm) REVERT: P 72 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7192 (tt0) REVERT: P 119 MET cc_start: 0.7841 (ttp) cc_final: 0.7610 (ttp) REVERT: P 176 MET cc_start: 0.8662 (mmp) cc_final: 0.8335 (mmm) REVERT: P 313 MET cc_start: 0.8229 (mmm) cc_final: 0.7796 (mmm) REVERT: P 326 LYS cc_start: 0.8325 (pttp) cc_final: 0.8014 (ptmm) REVERT: Q 44 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.7498 (mpt) REVERT: Q 47 MET cc_start: 0.8347 (mmm) cc_final: 0.7407 (ptt) REVERT: Q 103 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8192 (p) REVERT: Q 105 LEU cc_start: 0.8380 (mt) cc_final: 0.8093 (mt) REVERT: Q 269 MET cc_start: 0.8777 (ptm) cc_final: 0.8448 (ptm) REVERT: Q 291 LYS cc_start: 0.5847 (mttm) cc_final: 0.5246 (mmtt) REVERT: Q 326 LYS cc_start: 0.8022 (pttt) cc_final: 0.7618 (mmtm) REVERT: Q 372 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7506 (ptt90) REVERT: R 75 ILE cc_start: 0.8177 (pt) cc_final: 0.7905 (pt) REVERT: R 283 MET cc_start: 0.8433 (mmm) cc_final: 0.7695 (mmp) REVERT: R 286 ASP cc_start: 0.7507 (m-30) cc_final: 0.6997 (t0) REVERT: R 291 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8064 (mmtt) REVERT: R 352 PHE cc_start: 0.8501 (t80) cc_final: 0.7982 (t80) outliers start: 81 outliers final: 63 residues processed: 463 average time/residue: 1.0989 time to fit residues: 804.4284 Evaluate side-chains 460 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 386 time to evaluate : 4.736 ------------------------------------------------------------------------------- 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 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 141 SER 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 251 GLN 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 116 ARG 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 135 THR 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 F residue 160 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 211 ASP 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 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 54 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 162 ASN 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 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 456 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 345 optimal weight: 5.9990 chunk 267 optimal weight: 9.9990 chunk 398 optimal weight: 0.8980 chunk 264 optimal weight: 10.0000 chunk 471 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 I 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 39916 Z= 0.424 Angle : 0.634 7.410 54160 Z= 0.324 Chirality : 0.046 0.177 5990 Planarity : 0.004 0.050 6962 Dihedral : 8.828 149.518 5561 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.22 % Allowed : 11.58 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.12), residues: 4854 helix: -0.33 (0.12), residues: 2012 sheet: -1.19 (0.17), residues: 869 loop : -0.09 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 356 HIS 0.009 0.001 HIS E 156 PHE 0.018 0.002 PHE B 277 TYR 0.015 0.002 TYR D 75 ARG 0.006 0.001 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 479 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 386 time to evaluate : 4.702 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: 0.6976 (pm20) cc_final: 0.6550 (pm20) REVERT: A 137 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: A 188 ASP cc_start: 0.7305 (t0) cc_final: 0.7012 (t0) REVERT: A 276 HIS cc_start: 0.7667 (p90) cc_final: 0.6878 (p90) REVERT: A 363 MET cc_start: 0.7892 (mmm) cc_final: 0.7459 (mtp) REVERT: B 6 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7021 (mt) REVERT: B 51 ASP cc_start: 0.8015 (m-30) cc_final: 0.7386 (t0) REVERT: B 66 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7291 (tp40) REVERT: B 102 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6836 (ptpp) REVERT: B 224 GLU cc_start: 0.7545 (pt0) cc_final: 0.7225 (mt-10) REVERT: B 249 LYS cc_start: 0.8636 (mtmt) cc_final: 0.7972 (mtpp) REVERT: B 295 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6982 (ttm170) REVERT: B 361 MET cc_start: 0.8147 (ptp) cc_final: 0.7854 (ptm) REVERT: B 365 ASP cc_start: 0.8138 (t0) cc_final: 0.7821 (m-30) REVERT: C 55 ASP cc_start: 0.7916 (t0) cc_final: 0.7292 (m-30) REVERT: C 157 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7122 (p0) REVERT: C 183 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7866 (mmmm) REVERT: C 251 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: D 1 MET cc_start: 0.8681 (ptt) cc_final: 0.8384 (ptt) REVERT: D 105 GLU cc_start: 0.7134 (tt0) cc_final: 0.6884 (tm-30) REVERT: D 117 ASN cc_start: 0.8512 (m-40) cc_final: 0.7893 (m-40) REVERT: D 206 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7365 (mtm110) REVERT: D 230 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7376 (pt0) REVERT: E 79 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6819 (mt-10) REVERT: E 94 ARG cc_start: 0.7685 (mtp-110) cc_final: 0.7149 (mtm-85) REVERT: E 166 LYS cc_start: 0.8019 (mtpm) cc_final: 0.7611 (mmtt) REVERT: F 74 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8252 (pt) REVERT: F 88 ARG cc_start: 0.7604 (ttt-90) cc_final: 0.7238 (ttt-90) REVERT: G 30 GLU cc_start: 0.8261 (mp0) cc_final: 0.7586 (tm-30) REVERT: G 38 GLN cc_start: 0.8480 (tp40) cc_final: 0.8247 (tp-100) REVERT: G 88 ARG cc_start: 0.7607 (mmp80) cc_final: 0.6752 (mtm110) REVERT: G 124 SER cc_start: 0.7798 (t) cc_final: 0.7464 (m) REVERT: G 132 LYS cc_start: 0.7913 (mttm) cc_final: 0.7667 (mmmt) REVERT: H 12 ASN cc_start: 0.7989 (m-40) cc_final: 0.7774 (m-40) REVERT: H 68 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7325 (mttm) REVERT: H 100 GLU cc_start: 0.7268 (tt0) cc_final: 0.6805 (tm-30) REVERT: I 125 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7118 (mt-10) REVERT: M 90 PHE cc_start: 0.8125 (m-80) cc_final: 0.7794 (m-80) REVERT: M 123 MET cc_start: 0.8734 (mmt) cc_final: 0.8360 (mmt) REVERT: M 167 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7306 (tm-30) REVERT: M 207 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8134 (mm-30) REVERT: N 54 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8087 (m) REVERT: O 57 GLU cc_start: 0.7469 (tt0) cc_final: 0.7095 (tp30) REVERT: O 222 ASP cc_start: 0.8057 (t0) cc_final: 0.7493 (p0) REVERT: O 283 MET cc_start: 0.8771 (mmm) cc_final: 0.8406 (mmt) REVERT: O 287 ILE cc_start: 0.8797 (tt) cc_final: 0.8277 (mt) REVERT: P 72 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7203 (tt0) REVERT: P 176 MET cc_start: 0.8652 (mmp) cc_final: 0.8344 (mmm) REVERT: P 313 MET cc_start: 0.8232 (mmm) cc_final: 0.7823 (mmm) REVERT: P 326 LYS cc_start: 0.8366 (pttp) cc_final: 0.8050 (ptmm) REVERT: Q 44 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.7503 (mpt) REVERT: Q 47 MET cc_start: 0.8319 (mmm) cc_final: 0.7437 (ptt) REVERT: Q 103 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8213 (p) REVERT: Q 105 LEU cc_start: 0.8366 (mt) cc_final: 0.8084 (mt) REVERT: Q 291 LYS cc_start: 0.5850 (mttm) cc_final: 0.5082 (mmtt) REVERT: Q 326 LYS cc_start: 0.8067 (pttt) cc_final: 0.7640 (mmtm) REVERT: Q 372 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7201 (ptt90) REVERT: R 75 ILE cc_start: 0.8215 (pt) cc_final: 0.7931 (pt) REVERT: R 286 ASP cc_start: 0.7391 (m-30) cc_final: 0.6859 (t0) REVERT: R 291 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8050 (mmtt) REVERT: R 352 PHE cc_start: 0.8493 (t80) cc_final: 0.7977 (t80) outliers start: 93 outliers final: 71 residues processed: 459 average time/residue: 1.1120 time to fit residues: 811.9366 Evaluate side-chains 457 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 374 time to evaluate : 4.583 ------------------------------------------------------------------------------- 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 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 141 SER 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 251 GLN 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 C residue 356 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 159 ILE 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 45 ASP 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 74 ILE Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 19 GLN 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 149 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 173 HIS 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 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 328 LYS Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 89 THR 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 103 THR Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 277 THR Chi-restraints excluded: chain Q residue 372 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 203 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 291 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 299 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 370 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 D 143 ASN E 156 HIS M 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3959 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= 0.228 Angle : 0.575 6.929 54160 Z= 0.289 Chirality : 0.044 0.161 5990 Planarity : 0.004 0.050 6962 Dihedral : 8.579 151.883 5561 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.98 % Allowed : 11.96 % Favored : 86.06 % 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: -0.52 (0.12), residues: 4854 helix: -0.13 (0.12), residues: 2016 sheet: -0.95 (0.16), residues: 946 loop : 0.03 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 356 HIS 0.008 0.001 HIS E 156 PHE 0.015 0.001 PHE B 277 TYR 0.018 0.001 TYR I 279 ARG 0.006 0.000 ARG P 28 *********************** 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 488 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 405 time to evaluate : 5.214 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: 0.6904 (pm20) cc_final: 0.6511 (pm20) REVERT: A 137 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 188 ASP cc_start: 0.7301 (t70) cc_final: 0.6987 (t0) REVERT: A 276 HIS cc_start: 0.7591 (p90) cc_final: 0.6787 (p90) REVERT: A 363 MET cc_start: 0.7872 (mmm) cc_final: 0.7519 (mtp) REVERT: B 51 ASP cc_start: 0.8007 (m-30) cc_final: 0.7386 (t0) REVERT: B 66 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: B 102 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6790 (ptpp) REVERT: B 224 GLU cc_start: 0.7445 (pt0) cc_final: 0.7191 (mt-10) REVERT: B 249 LYS cc_start: 0.8602 (mtmt) cc_final: 0.7938 (mtpp) REVERT: B 295 ARG cc_start: 0.7471 (mtp180) cc_final: 0.6942 (ttm170) REVERT: B 365 ASP cc_start: 0.8117 (t0) cc_final: 0.7807 (m-30) REVERT: C 55 ASP cc_start: 0.7882 (t0) cc_final: 0.7261 (m-30) REVERT: C 157 ASN cc_start: 0.7379 (OUTLIER) cc_final: 0.7067 (p0) REVERT: C 183 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7857 (mmmm) REVERT: C 251 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: D 1 MET cc_start: 0.8709 (ptt) cc_final: 0.8393 (ptt) REVERT: D 103 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7246 (mt-10) REVERT: D 105 GLU cc_start: 0.7038 (tt0) cc_final: 0.6796 (tm-30) REVERT: D 117 ASN cc_start: 0.8436 (m-40) cc_final: 0.7716 (m110) REVERT: D 206 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7376 (mtm110) REVERT: D 230 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7386 (pt0) REVERT: D 247 GLU cc_start: 0.8126 (tp30) cc_final: 0.7731 (tt0) REVERT: E 79 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6804 (mt-10) REVERT: E 94 ARG cc_start: 0.7659 (mtp-110) cc_final: 0.7416 (mtm110) REVERT: E 166 LYS cc_start: 0.8011 (mtpm) cc_final: 0.7572 (mmtt) REVERT: F 74 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8121 (pt) REVERT: F 88 ARG cc_start: 0.7543 (ttt-90) cc_final: 0.7199 (ttt-90) REVERT: G 30 GLU cc_start: 0.8256 (mp0) cc_final: 0.7592 (tm-30) REVERT: G 38 GLN cc_start: 0.8518 (tp40) cc_final: 0.8316 (tp-100) REVERT: G 88 ARG cc_start: 0.7659 (mmp80) cc_final: 0.6653 (mtp85) REVERT: G 124 SER cc_start: 0.7744 (t) cc_final: 0.7432 (m) REVERT: G 132 LYS cc_start: 0.7893 (mttm) cc_final: 0.7664 (mmmt) REVERT: H 68 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7337 (mttm) REVERT: H 100 GLU cc_start: 0.7256 (tt0) cc_final: 0.6799 (tm-30) REVERT: H 132 MET cc_start: 0.8283 (ppp) cc_final: 0.7853 (tmm) REVERT: I 125 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7080 (mt-10) REVERT: I 355 MET cc_start: 0.7375 (mtt) cc_final: 0.7052 (mtt) REVERT: M 90 PHE cc_start: 0.8098 (m-80) cc_final: 0.7850 (m-80) REVERT: M 123 MET cc_start: 0.8715 (mmt) cc_final: 0.8336 (mmt) REVERT: M 167 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7287 (tm-30) REVERT: M 207 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8097 (mm-30) REVERT: M 279 TYR cc_start: 0.8764 (t80) cc_final: 0.8395 (t80) REVERT: O 57 GLU cc_start: 0.7443 (tt0) cc_final: 0.7102 (tp30) REVERT: O 222 ASP cc_start: 0.8031 (t0) cc_final: 0.7477 (p0) REVERT: O 283 MET cc_start: 0.8740 (mmm) cc_final: 0.8366 (mmt) REVERT: O 287 ILE cc_start: 0.8784 (tt) cc_final: 0.8284 (mt) REVERT: P 72 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7131 (tt0) REVERT: P 176 MET cc_start: 0.8670 (mmp) cc_final: 0.8378 (mmm) REVERT: P 313 MET cc_start: 0.8184 (mmm) cc_final: 0.7746 (mmm) REVERT: P 326 LYS cc_start: 0.8320 (pttp) cc_final: 0.8012 (ptmm) REVERT: Q 44 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.7495 (mpt) REVERT: Q 47 MET cc_start: 0.8259 (mmm) cc_final: 0.7452 (ptt) REVERT: Q 103 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8155 (p) REVERT: Q 105 LEU cc_start: 0.8336 (mt) cc_final: 0.8017 (mt) REVERT: Q 326 LYS cc_start: 0.8013 (pttt) cc_final: 0.7600 (mmtm) REVERT: Q 372 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7174 (ptt90) REVERT: R 68 LYS cc_start: 0.8338 (mtpp) cc_final: 0.8114 (mtmm) REVERT: R 75 ILE cc_start: 0.8169 (pt) cc_final: 0.7905 (pt) REVERT: R 286 ASP cc_start: 0.7361 (m-30) cc_final: 0.6898 (t0) REVERT: R 291 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8062 (mmtt) REVERT: R 352 PHE cc_start: 0.8477 (t80) cc_final: 0.7995 (t80) outliers start: 83 outliers final: 63 residues processed: 466 average time/residue: 1.1170 time to fit residues: 823.4437 Evaluate side-chains 463 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 389 time to evaluate : 4.669 ------------------------------------------------------------------------------- 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 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 125 SER Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 251 GLN 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 27 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU 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 F residue 160 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 H residue 211 ASP 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 173 HIS Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 89 THR 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 328 LYS 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 299 MET Chi-restraints excluded: chain P residue 344 SER 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 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 428 optimal weight: 3.9990 chunk 451 optimal weight: 2.9990 chunk 411 optimal weight: 5.9990 chunk 439 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 344 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 396 optimal weight: 0.7980 chunk 415 optimal weight: 4.9990 chunk 437 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39916 Z= 0.192 Angle : 0.557 6.982 54160 Z= 0.278 Chirality : 0.043 0.154 5990 Planarity : 0.004 0.050 6962 Dihedral : 8.369 154.957 5558 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.86 % Allowed : 12.22 % Favored : 85.92 % 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: -0.36 (0.12), residues: 4854 helix: 0.04 (0.12), residues: 2019 sheet: -0.97 (0.17), residues: 864 loop : 0.09 (0.15), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 356 HIS 0.008 0.001 HIS E 156 PHE 0.013 0.001 PHE B 277 TYR 0.013 0.001 TYR B 255 ARG 0.007 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 487 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 409 time to evaluate : 4.564 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 137 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: A 188 ASP cc_start: 0.7397 (t70) cc_final: 0.6992 (t0) REVERT: A 276 HIS cc_start: 0.7518 (p90) cc_final: 0.6733 (p90) REVERT: A 363 MET cc_start: 0.7815 (mmm) cc_final: 0.7501 (mtp) REVERT: B 51 ASP cc_start: 0.7978 (m-30) cc_final: 0.7382 (t0) REVERT: B 66 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7241 (tp40) REVERT: B 102 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6764 (ptpp) REVERT: B 224 GLU cc_start: 0.7376 (pt0) cc_final: 0.7158 (mt-10) REVERT: B 249 LYS cc_start: 0.8622 (mtmt) cc_final: 0.7958 (mtpp) REVERT: B 295 ARG cc_start: 0.7451 (mtp180) cc_final: 0.6919 (ttm170) REVERT: B 341 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 365 ASP cc_start: 0.8100 (t0) cc_final: 0.7797 (m-30) REVERT: C 55 ASP cc_start: 0.7889 (t0) cc_final: 0.7273 (m-30) REVERT: C 157 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7087 (p0) REVERT: C 183 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7847 (mmmm) REVERT: D 1 MET cc_start: 0.8608 (ptt) cc_final: 0.8321 (ptt) REVERT: D 103 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: D 105 GLU cc_start: 0.7072 (tt0) cc_final: 0.6774 (tm-30) REVERT: D 117 ASN cc_start: 0.8409 (m-40) cc_final: 0.7729 (m110) REVERT: D 206 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7345 (mtm110) REVERT: D 230 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7397 (pt0) REVERT: D 247 GLU cc_start: 0.8117 (tp30) cc_final: 0.7727 (tt0) REVERT: E 79 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6893 (mt-10) REVERT: E 94 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7479 (mtm110) REVERT: E 166 LYS cc_start: 0.8004 (mtpm) cc_final: 0.7563 (mmtt) REVERT: F 74 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8168 (pt) REVERT: F 88 ARG cc_start: 0.7534 (ttt-90) cc_final: 0.7199 (ttt-90) REVERT: G 30 GLU cc_start: 0.8236 (mp0) cc_final: 0.7558 (tm-30) REVERT: G 88 ARG cc_start: 0.7632 (mmp80) cc_final: 0.6649 (mtp85) REVERT: G 124 SER cc_start: 0.7730 (t) cc_final: 0.7432 (m) REVERT: G 132 LYS cc_start: 0.7936 (mttm) cc_final: 0.7704 (mmmt) REVERT: H 68 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7394 (mttm) REVERT: H 132 MET cc_start: 0.8273 (ppp) cc_final: 0.7865 (tmm) REVERT: I 125 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7275 (mt-10) REVERT: I 355 MET cc_start: 0.7370 (mtt) cc_final: 0.7046 (mtt) REVERT: M 90 PHE cc_start: 0.8069 (m-80) cc_final: 0.7851 (m-80) REVERT: M 123 MET cc_start: 0.8756 (mmt) cc_final: 0.8365 (mmt) REVERT: M 167 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7092 (tm-30) REVERT: M 207 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8062 (mm-30) REVERT: M 279 TYR cc_start: 0.8752 (t80) cc_final: 0.8366 (t80) REVERT: O 57 GLU cc_start: 0.7410 (tt0) cc_final: 0.7102 (tp30) REVERT: O 222 ASP cc_start: 0.8102 (t0) cc_final: 0.7484 (p0) REVERT: O 283 MET cc_start: 0.8727 (mmm) cc_final: 0.8321 (mmt) REVERT: O 287 ILE cc_start: 0.8772 (tt) cc_final: 0.8286 (mt) REVERT: P 72 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7117 (tt0) REVERT: P 125 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: P 176 MET cc_start: 0.8657 (mmp) cc_final: 0.8373 (mmm) REVERT: P 313 MET cc_start: 0.8157 (mmm) cc_final: 0.7714 (mmm) REVERT: P 326 LYS cc_start: 0.8163 (pttp) cc_final: 0.7838 (ptmm) REVERT: Q 44 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7464 (mpt) REVERT: Q 47 MET cc_start: 0.8245 (mmm) cc_final: 0.7445 (ptt) REVERT: Q 54 VAL cc_start: 0.9418 (p) cc_final: 0.9159 (t) REVERT: Q 103 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8162 (p) REVERT: Q 105 LEU cc_start: 0.8360 (mt) cc_final: 0.8040 (mt) REVERT: Q 326 LYS cc_start: 0.8031 (pttt) cc_final: 0.7603 (mmtm) REVERT: Q 372 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7485 (ptt90) REVERT: R 68 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8044 (mtmm) REVERT: R 283 MET cc_start: 0.8511 (mmm) cc_final: 0.7846 (mmp) REVERT: R 286 ASP cc_start: 0.7342 (m-30) cc_final: 0.6890 (t0) REVERT: R 291 LYS cc_start: 0.8426 (ttpp) cc_final: 0.8086 (mmtt) REVERT: R 352 PHE cc_start: 0.8453 (t80) cc_final: 0.7999 (t80) outliers start: 78 outliers final: 57 residues processed: 467 average time/residue: 1.0963 time to fit residues: 812.1410 Evaluate side-chains 459 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 390 time to evaluate : 4.572 ------------------------------------------------------------------------------- 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 38 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 72 GLU 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 333 LEU Chi-restraints excluded: chain B residue 341 GLU 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 346 MET 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 90 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU 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 30 VAL Chi-restraints excluded: chain H residue 34 ILE 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 119 MET Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 349 LEU Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 257 CYS 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 125 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 299 MET Chi-restraints excluded: chain P residue 344 SER 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 203 THR Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 288 optimal weight: 8.9990 chunk 464 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 322 optimal weight: 2.9990 chunk 487 optimal weight: 0.7980 chunk 448 optimal weight: 2.9990 chunk 387 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 39916 Z= 0.229 Angle : 0.562 7.096 54160 Z= 0.280 Chirality : 0.043 0.152 5990 Planarity : 0.004 0.049 6962 Dihedral : 8.322 153.696 5558 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.83 % Allowed : 12.34 % Favored : 85.83 % 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: -0.29 (0.12), residues: 4854 helix: 0.11 (0.12), residues: 2018 sheet: -0.93 (0.17), residues: 860 loop : 0.11 (0.15), residues: 1976 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 0.014 0.001 TYR R 294 ARG 0.007 0.000 ARG P 28 ********************** 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 475 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 398 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: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: A 188 ASP cc_start: 0.7435 (t70) cc_final: 0.7027 (t0) REVERT: A 276 HIS cc_start: 0.7489 (p90) cc_final: 0.6734 (p90) REVERT: A 363 MET cc_start: 0.7807 (mmm) cc_final: 0.7508 (mtp) REVERT: B 51 ASP cc_start: 0.7990 (m-30) cc_final: 0.7380 (t0) REVERT: B 66 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7247 (tp40) REVERT: B 102 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6761 (ptpp) REVERT: B 224 GLU cc_start: 0.7345 (pt0) cc_final: 0.7130 (mt-10) REVERT: B 249 LYS cc_start: 0.8685 (mtmt) cc_final: 0.7988 (mtpp) REVERT: B 295 ARG cc_start: 0.7413 (mtp180) cc_final: 0.6890 (ttm170) REVERT: B 341 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: B 365 ASP cc_start: 0.8098 (t0) cc_final: 0.7796 (m-30) REVERT: C 55 ASP cc_start: 0.7886 (t0) cc_final: 0.7257 (m-30) REVERT: C 157 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6940 (p0) REVERT: C 183 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7846 (mmmm) REVERT: C 251 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: D 1 MET cc_start: 0.8591 (ptt) cc_final: 0.8261 (ptt) REVERT: D 103 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: D 105 GLU cc_start: 0.7119 (tt0) cc_final: 0.6831 (tm-30) REVERT: D 117 ASN cc_start: 0.8390 (m-40) cc_final: 0.7712 (m110) REVERT: D 206 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7463 (mtm110) REVERT: D 230 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7419 (pt0) REVERT: E 79 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6901 (mt-10) REVERT: E 94 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7233 (mtm-85) REVERT: E 166 LYS cc_start: 0.8009 (mtpm) cc_final: 0.7562 (mmtt) REVERT: F 74 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8167 (pt) REVERT: F 88 ARG cc_start: 0.7515 (ttt-90) cc_final: 0.7183 (ttt-90) REVERT: G 30 GLU cc_start: 0.8251 (mp0) cc_final: 0.7573 (tm-30) REVERT: G 88 ARG cc_start: 0.7634 (mmp80) cc_final: 0.6648 (mtp85) REVERT: G 124 SER cc_start: 0.7748 (t) cc_final: 0.7449 (m) REVERT: G 132 LYS cc_start: 0.7925 (mttm) cc_final: 0.7696 (mmmt) REVERT: H 68 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7400 (mttm) REVERT: H 132 MET cc_start: 0.8271 (ppp) cc_final: 0.7867 (tmm) REVERT: I 125 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7062 (mt-10) REVERT: I 355 MET cc_start: 0.7371 (mtt) cc_final: 0.7064 (mtt) REVERT: M 90 PHE cc_start: 0.8064 (m-80) cc_final: 0.7851 (m-80) REVERT: M 123 MET cc_start: 0.8752 (mmt) cc_final: 0.8420 (mmt) REVERT: M 167 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7112 (tm-30) REVERT: M 207 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8169 (mm-30) REVERT: M 279 TYR cc_start: 0.8739 (t80) cc_final: 0.8359 (t80) REVERT: O 57 GLU cc_start: 0.7417 (tt0) cc_final: 0.7112 (tp30) REVERT: O 222 ASP cc_start: 0.8106 (t0) cc_final: 0.7477 (p0) REVERT: O 283 MET cc_start: 0.8733 (mmm) cc_final: 0.8356 (mmt) REVERT: O 286 ASP cc_start: 0.7685 (t0) cc_final: 0.7309 (m-30) REVERT: O 287 ILE cc_start: 0.8781 (tt) cc_final: 0.8333 (mt) REVERT: O 325 MET cc_start: 0.7452 (ptm) cc_final: 0.7049 (ptm) REVERT: P 72 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7114 (tt0) REVERT: P 125 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: P 176 MET cc_start: 0.8653 (mmp) cc_final: 0.8374 (mmm) REVERT: P 313 MET cc_start: 0.8167 (mmm) cc_final: 0.7733 (mmm) REVERT: P 326 LYS cc_start: 0.8173 (pttp) cc_final: 0.7853 (ptmm) REVERT: Q 44 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7450 (mpt) REVERT: Q 47 MET cc_start: 0.8255 (mmm) cc_final: 0.7448 (ptt) REVERT: Q 54 VAL cc_start: 0.9419 (p) cc_final: 0.9156 (t) REVERT: Q 103 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8168 (p) REVERT: Q 105 LEU cc_start: 0.8381 (mt) cc_final: 0.8097 (mt) REVERT: Q 326 LYS cc_start: 0.8052 (pttt) cc_final: 0.7607 (mmtm) REVERT: Q 372 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7543 (ptt90) REVERT: R 68 LYS cc_start: 0.8327 (mtpp) cc_final: 0.7947 (mtmm) REVERT: R 283 MET cc_start: 0.8456 (mmm) cc_final: 0.7791 (mmp) REVERT: R 286 ASP cc_start: 0.7359 (m-30) cc_final: 0.6917 (t0) REVERT: R 291 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8078 (mmtt) REVERT: R 352 PHE cc_start: 0.8338 (t80) cc_final: 0.7886 (t80) outliers start: 77 outliers final: 58 residues processed: 456 average time/residue: 1.0822 time to fit residues: 782.2293 Evaluate side-chains 455 residues out of total 4203 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 384 time to evaluate : 4.587 ------------------------------------------------------------------------------- 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 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 38 LEU Chi-restraints excluded: chain B residue 53 MET 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 333 LEU Chi-restraints excluded: chain B residue 341 GLU 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 251 GLN 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 27 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 225 GLU 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 H residue 211 ASP Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain I residue 18 LYS 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 M residue 85 ILE Chi-restraints excluded: chain M residue 89 THR 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 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 125 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 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 194 THR Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 308 optimal weight: 6.9990 chunk 413 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 398 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 N 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097539 restraints weight = 177651.803| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.93 r_work: 0.3116 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4198 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= 0.185 Angle : 0.547 7.408 54160 Z= 0.271 Chirality : 0.043 0.145 5990 Planarity : 0.004 0.052 6962 Dihedral : 8.177 155.416 5556 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.57 % Allowed : 12.55 % Favored : 85.87 % 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: -0.16 (0.12), residues: 4854 helix: 0.23 (0.12), residues: 2019 sheet: -0.89 (0.17), residues: 860 loop : 0.17 (0.15), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 356 HIS 0.008 0.001 HIS E 156 PHE 0.013 0.001 PHE B 277 TYR 0.014 0.001 TYR B 255 ARG 0.007 0.000 ARG P 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16711.14 seconds wall clock time: 285 minutes 34.51 seconds (17134.51 seconds total)