Starting phenix.real_space_refine on Wed Nov 20 00:48:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/11_2024/8f8s_28935.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/11_2024/8f8s_28935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/11_2024/8f8s_28935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/11_2024/8f8s_28935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/11_2024/8f8s_28935.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8s_28935/11_2024/8f8s_28935.cif" } resolution = 2.84 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= 0.001 sd= 0.018 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: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 7 5.21 5 S 143 5.16 5 C 12848 2.51 5 N 3434 2.21 5 O 3925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20371 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2811 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 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: "B" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2819 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 1 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: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.56, per 1000 atoms: 0.67 Number of scatterers: 20371 At special positions: 0 Unit cell: (84.24, 104.76, 241.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 14 15.00 Mg 7 11.99 O 3925 8.00 N 3434 7.00 C 12848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.8 seconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4778 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 40 sheets defined 49.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.673A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.507A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.520A pdb=" N ASP A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.648A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.834A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.776A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.512A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.053A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.616A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.065A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.506A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.895A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.576A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.501A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.998A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 removed outlier: 3.602A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.635A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.753A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.542A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.525A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.249A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.624A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.638A pdb=" N ASP B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.086A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.836A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.064A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.839A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.758A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.702A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.189A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.912A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.039A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.532A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.696A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.555A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.538A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.628A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.018A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.709A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.606A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.323A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.976A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.511A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.989A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.718A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.521A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.621A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.212A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.032A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.651A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.674A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 295 Processing helix chain 'G' and resid 302 through 306 removed outlier: 4.079A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 4.135A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.496A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.989A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.749A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 250 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.573A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 103 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.090A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.885A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.082A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.443A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.627A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC2, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.522A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.012A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.462A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 176 through 178 removed outlier: 3.798A pdb=" N GLN G 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.584A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.636A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD8, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.961A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE2, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.634A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 238 through 241 1015 hydrogen bonds defined for protein. 2619 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: 8.30 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6603 1.34 - 1.46: 3207 1.46 - 1.57: 10733 1.57 - 1.69: 21 1.69 - 1.81: 251 Bond restraints: 20815 Sorted by residual: bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.44e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.38e+00 ... (remaining 20810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 27372 1.39 - 2.78: 614 2.78 - 4.17: 189 4.17 - 5.56: 50 5.56 - 6.95: 29 Bond angle restraints: 28254 Sorted by residual: angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.24 -5.74 1.70e+00 3.46e-01 1.14e+01 angle pdb=" N HIC F 73 " pdb=" CA HIC F 73 " pdb=" CB HIC F 73 " ideal model delta sigma weight residual 110.50 115.82 -5.32 1.70e+00 3.46e-01 9.79e+00 angle pdb=" N HIC E 73 " pdb=" CA HIC E 73 " pdb=" CB HIC E 73 " ideal model delta sigma weight residual 110.50 115.78 -5.28 1.70e+00 3.46e-01 9.64e+00 angle pdb=" C ILE B 71 " pdb=" N GLU B 72 " pdb=" CA GLU B 72 " ideal model delta sigma weight residual 121.70 127.12 -5.42 1.80e+00 3.09e-01 9.05e+00 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 115.55 -5.05 1.70e+00 3.46e-01 8.84e+00 ... (remaining 28249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 12206 33.77 - 67.54: 294 67.54 - 101.31: 11 101.31 - 135.08: 7 135.08 - 168.85: 2 Dihedral angle restraints: 12520 sinusoidal: 5060 harmonic: 7460 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.86 -168.85 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.96 -147.96 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 65.95 -125.95 1 2.00e+01 2.50e-03 3.81e+01 ... (remaining 12517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1590 0.029 - 0.057: 945 0.057 - 0.086: 342 0.086 - 0.114: 216 0.114 - 0.143: 48 Chirality restraints: 3141 Sorted by residual: chirality pdb=" CA ILE G 165 " pdb=" N ILE G 165 " pdb=" C ILE G 165 " pdb=" CB ILE G 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE F 165 " pdb=" N ILE F 165 " pdb=" C ILE F 165 " pdb=" CB ILE F 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE C 165 " pdb=" N ILE C 165 " pdb=" C ILE C 165 " pdb=" CB ILE C 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 3138 not shown) Planarity restraints: 3609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 322 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 321 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO E 322 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 322 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 322 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 321 " 0.041 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO F 322 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 322 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 322 " 0.035 5.00e-02 4.00e+02 ... (remaining 3606 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 139 2.58 - 3.16: 15570 3.16 - 3.74: 31433 3.74 - 4.32: 45129 4.32 - 4.90: 75663 Nonbonded interactions: 167934 Sorted by model distance: nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.002 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.039 2.170 nonbonded pdb=" O3B ADP G 401 " pdb="MG MG G 402 " model vdw 2.042 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.146 2.170 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.232 3.040 ... (remaining 167929 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 'A' selection = (chain 'B' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'C' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'D' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'E' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'F' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) selection = (chain 'G' and (resid 5 through 40 or resid 52 through 374 or resid 401 through \ 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 48.650 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.004 0.057 20815 Z= 0.244 Angle : 0.613 6.945 28254 Z= 0.306 Chirality : 0.046 0.143 3141 Planarity : 0.005 0.064 3609 Dihedral : 14.041 168.855 7742 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.94 % Allowed : 7.85 % Favored : 89.22 % 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: -0.35 (0.17), residues: 2540 helix: -0.79 (0.15), residues: 1065 sheet: 0.58 (0.24), residues: 473 loop : 0.29 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.005 0.001 HIS C 161 PHE 0.013 0.001 PHE D 255 TYR 0.012 0.001 TYR F 143 ARG 0.006 0.001 ARG F 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 621 time to evaluate : 2.307 Fit side-chains REVERT: A 61 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7920 (pttp) REVERT: A 71 ILE cc_start: 0.8137 (mm) cc_final: 0.7868 (mt) REVERT: A 82 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7613 (tpp) REVERT: A 94 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7575 (tm) REVERT: A 99 GLU cc_start: 0.7474 (mp0) cc_final: 0.7256 (mp0) REVERT: A 116 ARG cc_start: 0.7376 (ttp80) cc_final: 0.6710 (ttp80) REVERT: A 122 ILE cc_start: 0.8450 (mm) cc_final: 0.8236 (mp) REVERT: A 214 GLU cc_start: 0.7899 (tt0) cc_final: 0.7659 (mt-10) REVERT: A 215 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7772 (ttmm) REVERT: A 224 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7239 (tp30) REVERT: A 299 MET cc_start: 0.8651 (mtp) cc_final: 0.8323 (mtp) REVERT: A 316 GLU cc_start: 0.8736 (tp30) cc_final: 0.8497 (tp30) REVERT: A 355 MET cc_start: 0.7153 (mpp) cc_final: 0.6917 (mpp) REVERT: B 61 LYS cc_start: 0.8081 (mmtp) cc_final: 0.7832 (mmtp) REVERT: B 83 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: B 116 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7556 (ptm160) REVERT: B 117 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 118 LYS cc_start: 0.7876 (tptt) cc_final: 0.7620 (tptt) REVERT: B 184 ASP cc_start: 0.8086 (m-30) cc_final: 0.7874 (m-30) REVERT: B 205 GLU cc_start: 0.7378 (mp0) cc_final: 0.7145 (mp0) REVERT: B 207 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 248 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8092 (pt) REVERT: B 291 LYS cc_start: 0.8581 (tttp) cc_final: 0.8321 (tttm) REVERT: C 72 GLU cc_start: 0.7694 (tt0) cc_final: 0.7430 (tp30) REVERT: C 98 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8560 (Cg_endo) REVERT: C 99 GLU cc_start: 0.7518 (pm20) cc_final: 0.7273 (pm20) REVERT: C 118 LYS cc_start: 0.8423 (mtpp) cc_final: 0.8168 (mttm) REVERT: C 227 MET cc_start: 0.8814 (mmm) cc_final: 0.8607 (mmm) REVERT: C 334 GLU cc_start: 0.7734 (pm20) cc_final: 0.7434 (pm20) REVERT: D 44 MET cc_start: 0.7811 (tpp) cc_final: 0.7550 (tpp) REVERT: D 90 PHE cc_start: 0.8594 (m-80) cc_final: 0.8360 (m-80) REVERT: D 117 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7793 (mt-10) REVERT: D 227 MET cc_start: 0.8516 (mmm) cc_final: 0.8313 (mmp) REVERT: D 284 LYS cc_start: 0.8571 (mttp) cc_final: 0.8328 (mtpm) REVERT: E 99 GLU cc_start: 0.7566 (pm20) cc_final: 0.7298 (pp20) REVERT: E 121 GLN cc_start: 0.8395 (tt0) cc_final: 0.8146 (tt0) REVERT: E 147 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8716 (ptp-170) REVERT: E 288 ASP cc_start: 0.7758 (m-30) cc_final: 0.7499 (m-30) REVERT: E 313 MET cc_start: 0.8488 (mmm) cc_final: 0.8219 (tpt) REVERT: E 337 TYR cc_start: 0.8774 (m-10) cc_final: 0.8568 (m-80) REVERT: F 68 LYS cc_start: 0.8708 (mmtp) cc_final: 0.8453 (mmtp) REVERT: F 96 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8554 (m) REVERT: F 99 GLU cc_start: 0.7742 (mp0) cc_final: 0.7410 (mp0) REVERT: F 167 GLU cc_start: 0.8039 (mp0) cc_final: 0.7820 (mp0) REVERT: F 210 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7999 (ttm110) REVERT: F 222 ASP cc_start: 0.7979 (t0) cc_final: 0.7745 (t0) REVERT: F 354 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7244 (mm-40) REVERT: F 355 MET cc_start: 0.8216 (mtp) cc_final: 0.8002 (mtm) REVERT: F 364 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7248 (mm-30) REVERT: F 373 LYS cc_start: 0.8625 (tttp) cc_final: 0.8246 (mtpt) REVERT: G 117 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: G 147 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7907 (ptm160) REVERT: G 270 GLU cc_start: 0.6394 (mp0) cc_final: 0.5622 (mp0) REVERT: G 283 MET cc_start: 0.8209 (mmt) cc_final: 0.7760 (mmt) REVERT: G 311 ASP cc_start: 0.7838 (p0) cc_final: 0.7584 (p0) outliers start: 64 outliers final: 21 residues processed: 654 average time/residue: 1.6485 time to fit residues: 1191.5064 Evaluate side-chains 620 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 589 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.0370 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 111 ASN B 115 ASN B 297 ASN B 360 GLN C 12 ASN C 137 GLN C 246 GLN C 371 HIS D 12 ASN D 137 GLN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 246 GLN F 297 ASN G 12 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20815 Z= 0.287 Angle : 0.644 8.308 28254 Z= 0.316 Chirality : 0.047 0.219 3141 Planarity : 0.005 0.056 3609 Dihedral : 10.658 166.971 2967 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.08 % Allowed : 15.60 % Favored : 80.31 % 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: 0.00 (0.17), residues: 2540 helix: -0.22 (0.16), residues: 1100 sheet: 0.54 (0.24), residues: 471 loop : 0.27 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.004 0.001 HIS C 161 PHE 0.016 0.001 PHE A 223 TYR 0.016 0.001 TYR A 198 ARG 0.007 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 593 time to evaluate : 2.345 Fit side-chains REVERT: A 61 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7860 (pttp) REVERT: A 81 ASP cc_start: 0.7812 (p0) cc_final: 0.7225 (p0) REVERT: A 82 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7488 (tpp) REVERT: A 99 GLU cc_start: 0.7539 (mp0) cc_final: 0.7321 (mp0) REVERT: A 167 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7874 (tp30) REVERT: A 214 GLU cc_start: 0.7832 (tt0) cc_final: 0.7535 (mt-10) REVERT: A 215 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7896 (ttmm) REVERT: A 254 ARG cc_start: 0.8358 (mtp85) cc_final: 0.8051 (mtp180) REVERT: A 299 MET cc_start: 0.8567 (mtp) cc_final: 0.8220 (mtp) REVERT: A 316 GLU cc_start: 0.8783 (tp30) cc_final: 0.8521 (tp30) REVERT: B 21 PHE cc_start: 0.8600 (m-80) cc_final: 0.8300 (m-80) REVERT: B 61 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7841 (mmtp) REVERT: B 117 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 118 LYS cc_start: 0.7738 (tptt) cc_final: 0.7378 (tptt) REVERT: B 184 ASP cc_start: 0.8091 (m-30) cc_final: 0.7876 (m-30) REVERT: B 205 GLU cc_start: 0.7124 (mp0) cc_final: 0.6783 (mp0) REVERT: B 215 LYS cc_start: 0.8418 (mttp) cc_final: 0.8045 (mttp) REVERT: C 44 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7024 (mpp) REVERT: C 72 GLU cc_start: 0.7728 (tt0) cc_final: 0.7441 (tp30) REVERT: C 99 GLU cc_start: 0.7590 (pm20) cc_final: 0.7307 (pm20) REVERT: C 118 LYS cc_start: 0.8402 (mtpp) cc_final: 0.8163 (mttm) REVERT: C 224 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7844 (mm-30) REVERT: C 334 GLU cc_start: 0.7723 (pm20) cc_final: 0.7430 (pm20) REVERT: D 44 MET cc_start: 0.7866 (tpp) cc_final: 0.7508 (tpp) REVERT: D 90 PHE cc_start: 0.8548 (m-80) cc_final: 0.8335 (m-80) REVERT: D 117 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7786 (mt-10) REVERT: D 132 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8162 (ppp) REVERT: D 180 LEU cc_start: 0.8952 (tp) cc_final: 0.8738 (tt) REVERT: D 211 ASP cc_start: 0.8148 (t0) cc_final: 0.7904 (t0) REVERT: D 227 MET cc_start: 0.8547 (mmm) cc_final: 0.8344 (mmp) REVERT: D 284 LYS cc_start: 0.8571 (mttp) cc_final: 0.8292 (mtpm) REVERT: E 99 GLU cc_start: 0.7647 (pm20) cc_final: 0.7342 (pp20) REVERT: E 147 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8692 (ptp-170) REVERT: E 288 ASP cc_start: 0.7785 (m-30) cc_final: 0.7519 (m-30) REVERT: E 313 MET cc_start: 0.8505 (mmm) cc_final: 0.8213 (tpt) REVERT: F 68 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8439 (mmtp) REVERT: F 96 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8571 (m) REVERT: F 99 GLU cc_start: 0.7705 (mp0) cc_final: 0.7335 (mp0) REVERT: F 210 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8069 (ttm110) REVERT: F 354 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7247 (mm-40) REVERT: F 355 MET cc_start: 0.8260 (mtp) cc_final: 0.8033 (mtm) REVERT: F 364 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7229 (mm-30) REVERT: G 125 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: G 147 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8310 (ptm160) REVERT: G 222 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7422 (p0) REVERT: G 270 GLU cc_start: 0.6473 (mp0) cc_final: 0.5722 (mp0) REVERT: G 283 MET cc_start: 0.8177 (mmt) cc_final: 0.7827 (mmt) outliers start: 89 outliers final: 40 residues processed: 635 average time/residue: 1.6425 time to fit residues: 1152.8093 Evaluate side-chains 624 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 574 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS A 111 ASN A 115 ASN A 354 GLN B 111 ASN B 297 ASN C 12 ASN C 115 ASN C 137 GLN C 246 GLN D 12 ASN D 137 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 297 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 246 GLN F 59 GLN F 137 GLN F 246 GLN F 353 GLN G 12 ASN G 92 ASN G 115 ASN G 297 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20815 Z= 0.286 Angle : 0.629 7.612 28254 Z= 0.306 Chirality : 0.047 0.186 3141 Planarity : 0.005 0.055 3609 Dihedral : 10.328 169.337 2951 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.45 % Allowed : 17.44 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2540 helix: 0.04 (0.16), residues: 1105 sheet: 0.61 (0.24), residues: 462 loop : 0.23 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.014 0.001 PHE B 31 TYR 0.016 0.001 TYR A 198 ARG 0.008 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 589 time to evaluate : 2.215 Fit side-chains REVERT: A 18 LYS cc_start: 0.8278 (mptt) cc_final: 0.8042 (mptt) REVERT: A 61 LYS cc_start: 0.8209 (pttp) cc_final: 0.7820 (pttp) REVERT: A 81 ASP cc_start: 0.7849 (p0) cc_final: 0.7533 (p0) REVERT: A 99 GLU cc_start: 0.7525 (mp0) cc_final: 0.7259 (mp0) REVERT: A 115 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7980 (t0) REVERT: A 167 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7872 (tp30) REVERT: A 214 GLU cc_start: 0.7903 (tt0) cc_final: 0.7638 (mt-10) REVERT: A 215 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7892 (ttmm) REVERT: A 254 ARG cc_start: 0.8342 (mtp85) cc_final: 0.8051 (mtp180) REVERT: A 299 MET cc_start: 0.8546 (mtp) cc_final: 0.8340 (mtp) REVERT: A 316 GLU cc_start: 0.8775 (tp30) cc_final: 0.8493 (tp30) REVERT: B 21 PHE cc_start: 0.8597 (m-80) cc_final: 0.8320 (m-80) REVERT: B 61 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7843 (mmtp) REVERT: B 89 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8375 (t) REVERT: B 117 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6846 (mm-30) REVERT: B 118 LYS cc_start: 0.7777 (tptt) cc_final: 0.7432 (tptt) REVERT: B 205 GLU cc_start: 0.7318 (mp0) cc_final: 0.6928 (mp0) REVERT: B 215 LYS cc_start: 0.8435 (mttp) cc_final: 0.8219 (mtmm) REVERT: C 44 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7063 (mpp) REVERT: C 72 GLU cc_start: 0.7713 (tt0) cc_final: 0.7423 (tp30) REVERT: C 99 GLU cc_start: 0.7569 (pm20) cc_final: 0.7279 (pm20) REVERT: C 113 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8175 (mtmm) REVERT: C 118 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8203 (mttm) REVERT: C 297 ASN cc_start: 0.8577 (m110) cc_final: 0.8288 (m110) REVERT: C 334 GLU cc_start: 0.7745 (pm20) cc_final: 0.7439 (pm20) REVERT: D 90 PHE cc_start: 0.8546 (m-80) cc_final: 0.8342 (m-80) REVERT: D 117 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7775 (mt-10) REVERT: D 132 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7866 (ppp) REVERT: D 180 LEU cc_start: 0.8944 (tp) cc_final: 0.8730 (tt) REVERT: D 211 ASP cc_start: 0.8149 (t0) cc_final: 0.7886 (t0) REVERT: D 284 LYS cc_start: 0.8583 (mttp) cc_final: 0.8294 (mtpm) REVERT: E 59 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8220 (tp40) REVERT: E 99 GLU cc_start: 0.7641 (pm20) cc_final: 0.7404 (pp20) REVERT: E 147 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8633 (ptp-170) REVERT: E 288 ASP cc_start: 0.7795 (m-30) cc_final: 0.7505 (m-30) REVERT: E 313 MET cc_start: 0.8493 (mmm) cc_final: 0.8212 (tpp) REVERT: F 68 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8473 (mmtp) REVERT: F 96 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8585 (m) REVERT: F 99 GLU cc_start: 0.7730 (mp0) cc_final: 0.7337 (mp0) REVERT: F 210 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8078 (ttm110) REVERT: F 241 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: F 314 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: F 353 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7498 (mp-120) REVERT: F 354 GLN cc_start: 0.7469 (mm-40) cc_final: 0.7248 (mm-40) REVERT: F 355 MET cc_start: 0.8242 (mtp) cc_final: 0.7996 (mtm) REVERT: F 364 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7244 (mm-30) REVERT: G 147 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8319 (ptm160) REVERT: G 222 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7419 (p0) REVERT: G 270 GLU cc_start: 0.6485 (mp0) cc_final: 0.5760 (mp0) REVERT: G 283 MET cc_start: 0.8158 (mmt) cc_final: 0.7857 (mmt) REVERT: G 355 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7671 (mmm) outliers start: 97 outliers final: 42 residues processed: 633 average time/residue: 1.6515 time to fit residues: 1156.2335 Evaluate side-chains 643 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 586 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 355 MET Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.8980 chunk 175 optimal weight: 0.0970 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 221 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN B 111 ASN B 121 GLN B 297 ASN C 101 HIS C 128 ASN C 137 GLN C 162 ASN D 12 ASN D 115 ASN D 137 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 246 GLN G 12 ASN G 92 ASN G 115 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20815 Z= 0.220 Angle : 0.611 8.336 28254 Z= 0.294 Chirality : 0.046 0.160 3141 Planarity : 0.004 0.055 3609 Dihedral : 10.064 173.307 2941 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.04 % Allowed : 18.49 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2540 helix: 0.21 (0.16), residues: 1113 sheet: 0.69 (0.24), residues: 466 loop : 0.39 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE F 255 TYR 0.013 0.001 TYR A 198 ARG 0.009 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 590 time to evaluate : 2.332 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8197 (pttp) cc_final: 0.7825 (pttp) REVERT: A 99 GLU cc_start: 0.7522 (mp0) cc_final: 0.7258 (mp0) REVERT: A 167 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7909 (mm-30) REVERT: A 215 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7892 (ttmm) REVERT: A 254 ARG cc_start: 0.8319 (mtp85) cc_final: 0.8032 (mtp180) REVERT: A 299 MET cc_start: 0.8514 (mtp) cc_final: 0.8161 (mtm) REVERT: A 316 GLU cc_start: 0.8764 (tp30) cc_final: 0.8500 (tp30) REVERT: B 11 ASP cc_start: 0.8804 (t0) cc_final: 0.8340 (t70) REVERT: B 21 PHE cc_start: 0.8556 (m-80) cc_final: 0.8308 (m-80) REVERT: B 61 LYS cc_start: 0.8061 (mmtp) cc_final: 0.7837 (mmtp) REVERT: B 117 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6821 (mm-30) REVERT: B 118 LYS cc_start: 0.7768 (tptt) cc_final: 0.7430 (tptt) REVERT: B 205 GLU cc_start: 0.7340 (mp0) cc_final: 0.6931 (mp0) REVERT: B 207 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 215 LYS cc_start: 0.8464 (mttp) cc_final: 0.8160 (mtmm) REVERT: C 44 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7051 (mpp) REVERT: C 72 GLU cc_start: 0.7706 (tt0) cc_final: 0.7415 (tp30) REVERT: C 99 GLU cc_start: 0.7557 (pm20) cc_final: 0.7257 (pm20) REVERT: C 118 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8194 (mttm) REVERT: C 297 ASN cc_start: 0.8566 (m110) cc_final: 0.8264 (m110) REVERT: C 334 GLU cc_start: 0.7746 (pm20) cc_final: 0.7432 (pm20) REVERT: D 132 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7922 (ppp) REVERT: D 180 LEU cc_start: 0.8927 (tp) cc_final: 0.8723 (tt) REVERT: D 211 ASP cc_start: 0.8133 (t0) cc_final: 0.7919 (t0) REVERT: D 284 LYS cc_start: 0.8550 (mttp) cc_final: 0.8256 (mtpm) REVERT: E 99 GLU cc_start: 0.7636 (pm20) cc_final: 0.7407 (pp20) REVERT: E 288 ASP cc_start: 0.7788 (m-30) cc_final: 0.7493 (m-30) REVERT: E 313 MET cc_start: 0.8485 (mmm) cc_final: 0.8235 (mmm) REVERT: F 68 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8451 (mmtp) REVERT: F 96 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8587 (m) REVERT: F 99 GLU cc_start: 0.7731 (mp0) cc_final: 0.7288 (mp0) REVERT: F 113 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7681 (mmtp) REVERT: F 210 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8030 (ttm110) REVERT: F 314 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: F 354 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7241 (mm-40) REVERT: F 355 MET cc_start: 0.8251 (mtp) cc_final: 0.7997 (mtm) REVERT: F 364 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7235 (mm-30) REVERT: G 83 GLU cc_start: 0.7679 (tt0) cc_final: 0.7456 (tt0) REVERT: G 116 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7516 (ttm-80) REVERT: G 147 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8400 (ptm160) REVERT: G 222 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7360 (p0) REVERT: G 270 GLU cc_start: 0.6459 (mp0) cc_final: 0.5681 (mp0) outliers start: 88 outliers final: 45 residues processed: 627 average time/residue: 1.6552 time to fit residues: 1146.7699 Evaluate side-chains 639 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 585 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 222 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 12 ASN C 137 GLN C 162 ASN D 12 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 246 GLN G 12 ASN G 92 ASN G 115 ASN G 297 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20815 Z= 0.304 Angle : 0.638 8.280 28254 Z= 0.309 Chirality : 0.047 0.153 3141 Planarity : 0.005 0.057 3609 Dihedral : 10.113 179.471 2937 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.77 % Allowed : 18.27 % Favored : 76.96 % 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: 0.38 (0.17), residues: 2540 helix: 0.24 (0.16), residues: 1110 sheet: 0.64 (0.24), residues: 462 loop : 0.33 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.006 0.001 HIS C 101 PHE 0.012 0.001 PHE F 31 TYR 0.013 0.001 TYR B 362 ARG 0.009 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 589 time to evaluate : 2.391 Fit side-chains REVERT: A 18 LYS cc_start: 0.8193 (mptt) cc_final: 0.7942 (mptt) REVERT: A 61 LYS cc_start: 0.8195 (pttp) cc_final: 0.7810 (pttp) REVERT: A 82 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7360 (tpp) REVERT: A 99 GLU cc_start: 0.7554 (mp0) cc_final: 0.7285 (mp0) REVERT: A 115 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.8000 (t0) REVERT: A 167 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7982 (tp30) REVERT: A 214 GLU cc_start: 0.7881 (tt0) cc_final: 0.7649 (mt-10) REVERT: A 225 ASN cc_start: 0.8215 (t0) cc_final: 0.7751 (t0) REVERT: A 299 MET cc_start: 0.8545 (mtp) cc_final: 0.8146 (mtm) REVERT: A 316 GLU cc_start: 0.8755 (tp30) cc_final: 0.8474 (tp30) REVERT: A 361 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7034 (mt-10) REVERT: B 21 PHE cc_start: 0.8571 (m-80) cc_final: 0.8322 (m-80) REVERT: B 61 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7825 (mmtp) REVERT: B 89 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 117 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6817 (mm-30) REVERT: B 118 LYS cc_start: 0.7789 (tptt) cc_final: 0.7494 (tptt) REVERT: B 205 GLU cc_start: 0.7398 (mp0) cc_final: 0.6981 (mp0) REVERT: B 207 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 215 LYS cc_start: 0.8457 (mttp) cc_final: 0.8156 (mtmm) REVERT: C 44 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7040 (mpp) REVERT: C 72 GLU cc_start: 0.7706 (tt0) cc_final: 0.7423 (tp30) REVERT: C 99 GLU cc_start: 0.7558 (pm20) cc_final: 0.7240 (pm20) REVERT: C 113 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8185 (mtmm) REVERT: C 118 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8208 (mttm) REVERT: C 297 ASN cc_start: 0.8564 (m110) cc_final: 0.8279 (m110) REVERT: C 334 GLU cc_start: 0.7761 (pm20) cc_final: 0.7457 (pm20) REVERT: D 51 ASP cc_start: 0.7719 (p0) cc_final: 0.7519 (p0) REVERT: D 132 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7891 (ppp) REVERT: D 180 LEU cc_start: 0.8947 (tp) cc_final: 0.8726 (tt) REVERT: D 211 ASP cc_start: 0.8138 (t0) cc_final: 0.7881 (t0) REVERT: D 284 LYS cc_start: 0.8573 (mttp) cc_final: 0.8276 (mtpm) REVERT: E 59 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8179 (tp40) REVERT: E 99 GLU cc_start: 0.7649 (pm20) cc_final: 0.7417 (pp20) REVERT: E 205 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7453 (mt-10) REVERT: E 288 ASP cc_start: 0.7796 (m-30) cc_final: 0.7494 (m-30) REVERT: E 313 MET cc_start: 0.8470 (mmm) cc_final: 0.8265 (mmm) REVERT: F 99 GLU cc_start: 0.7744 (mp0) cc_final: 0.7341 (mp0) REVERT: F 113 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7688 (mmtp) REVERT: F 210 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8045 (ttm110) REVERT: F 241 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: F 314 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: F 354 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7283 (mm-40) REVERT: F 355 MET cc_start: 0.8229 (mtp) cc_final: 0.7978 (mtm) REVERT: G 116 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7509 (ttm-80) REVERT: G 125 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: G 147 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8349 (ptm160) REVERT: G 270 GLU cc_start: 0.6499 (mp0) cc_final: 0.4951 (tt0) outliers start: 104 outliers final: 51 residues processed: 634 average time/residue: 1.7413 time to fit residues: 1216.1187 Evaluate side-chains 651 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 586 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 326 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 145 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN B 12 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN D 12 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 161 HIS F 246 GLN G 12 ASN G 297 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20815 Z= 0.298 Angle : 0.644 10.091 28254 Z= 0.311 Chirality : 0.047 0.170 3141 Planarity : 0.005 0.060 3609 Dihedral : 10.025 176.298 2934 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.50 % Allowed : 20.19 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2540 helix: 0.32 (0.16), residues: 1095 sheet: 0.58 (0.24), residues: 466 loop : 0.31 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.005 0.001 HIS C 101 PHE 0.012 0.001 PHE F 31 TYR 0.014 0.001 TYR D 166 ARG 0.009 0.001 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 589 time to evaluate : 2.216 Fit side-chains REVERT: A 61 LYS cc_start: 0.8188 (pttp) cc_final: 0.7782 (pttp) REVERT: A 82 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7449 (tpp) REVERT: A 99 GLU cc_start: 0.7559 (mp0) cc_final: 0.7272 (mp0) REVERT: A 115 ASN cc_start: 0.8283 (t0) cc_final: 0.7999 (t0) REVERT: A 167 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 214 GLU cc_start: 0.7809 (tt0) cc_final: 0.7589 (mt-10) REVERT: A 225 ASN cc_start: 0.8216 (t0) cc_final: 0.7746 (t0) REVERT: A 265 SER cc_start: 0.8759 (m) cc_final: 0.8412 (t) REVERT: A 299 MET cc_start: 0.8545 (mtp) cc_final: 0.8208 (mtm) REVERT: A 316 GLU cc_start: 0.8748 (tp30) cc_final: 0.8471 (tp30) REVERT: A 361 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6829 (mt-10) REVERT: A 364 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6103 (pt0) REVERT: B 21 PHE cc_start: 0.8566 (m-80) cc_final: 0.8302 (m-80) REVERT: B 61 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7838 (mmtp) REVERT: B 89 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8227 (t) REVERT: B 117 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6795 (mm-30) REVERT: B 118 LYS cc_start: 0.7792 (tptt) cc_final: 0.7480 (tptt) REVERT: B 205 GLU cc_start: 0.7408 (mp0) cc_final: 0.6988 (mp0) REVERT: B 207 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 215 LYS cc_start: 0.8458 (mttp) cc_final: 0.8197 (mtmm) REVERT: B 291 LYS cc_start: 0.8536 (tttm) cc_final: 0.8296 (tttm) REVERT: C 44 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7038 (mpp) REVERT: C 72 GLU cc_start: 0.7702 (tt0) cc_final: 0.7417 (tp30) REVERT: C 99 GLU cc_start: 0.7569 (pm20) cc_final: 0.7251 (pm20) REVERT: C 113 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8177 (mtmm) REVERT: C 118 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8195 (mttm) REVERT: C 297 ASN cc_start: 0.8581 (m110) cc_final: 0.8291 (m110) REVERT: C 334 GLU cc_start: 0.7756 (pm20) cc_final: 0.7447 (pm20) REVERT: D 51 ASP cc_start: 0.7722 (p0) cc_final: 0.7520 (p0) REVERT: D 132 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7953 (ppp) REVERT: D 180 LEU cc_start: 0.8948 (tp) cc_final: 0.8733 (tt) REVERT: D 211 ASP cc_start: 0.8141 (t0) cc_final: 0.7881 (t0) REVERT: D 284 LYS cc_start: 0.8574 (mttp) cc_final: 0.8276 (mtpm) REVERT: E 99 GLU cc_start: 0.7644 (pm20) cc_final: 0.7420 (pp20) REVERT: E 205 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7448 (mt-10) REVERT: E 288 ASP cc_start: 0.7714 (m-30) cc_final: 0.7407 (m-30) REVERT: E 313 MET cc_start: 0.8470 (mmm) cc_final: 0.8265 (mmm) REVERT: F 99 GLU cc_start: 0.7741 (mp0) cc_final: 0.7334 (mp0) REVERT: F 113 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7682 (mmtp) REVERT: F 210 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8035 (ttm110) REVERT: F 241 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: F 314 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: F 354 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7295 (mm-40) REVERT: G 116 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7547 (ttm-80) REVERT: G 125 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: G 147 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8432 (ptm160) REVERT: G 238 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8352 (mtpt) REVERT: G 270 GLU cc_start: 0.6509 (mp0) cc_final: 0.4928 (tt0) REVERT: G 276 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7790 (mt-10) outliers start: 98 outliers final: 54 residues processed: 631 average time/residue: 1.7142 time to fit residues: 1191.4517 Evaluate side-chains 652 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 585 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 0.4980 chunk 208 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 154 optimal weight: 0.0770 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 12 ASN B 111 ASN B 173 HIS B 297 ASN C 137 GLN C 162 ASN D 12 ASN D 162 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 246 GLN G 12 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20815 Z= 0.199 Angle : 0.621 8.647 28254 Z= 0.296 Chirality : 0.046 0.212 3141 Planarity : 0.004 0.063 3609 Dihedral : 9.715 174.027 2934 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.31 % Allowed : 20.70 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2540 helix: 0.38 (0.16), residues: 1110 sheet: 0.60 (0.24), residues: 467 loop : 0.47 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.012 0.001 PHE F 255 TYR 0.011 0.001 TYR A 198 ARG 0.009 0.000 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 594 time to evaluate : 2.316 Fit side-chains REVERT: A 61 LYS cc_start: 0.8174 (pttp) cc_final: 0.7768 (pttp) REVERT: A 82 MET cc_start: 0.7651 (mmp) cc_final: 0.7374 (tpp) REVERT: A 99 GLU cc_start: 0.7562 (mp0) cc_final: 0.7266 (mp0) REVERT: A 167 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8018 (mm-30) REVERT: A 214 GLU cc_start: 0.7818 (tt0) cc_final: 0.7594 (mt-10) REVERT: A 225 ASN cc_start: 0.8221 (t0) cc_final: 0.7757 (t0) REVERT: A 265 SER cc_start: 0.8747 (m) cc_final: 0.8424 (t) REVERT: A 299 MET cc_start: 0.8535 (mtp) cc_final: 0.8186 (mtm) REVERT: A 316 GLU cc_start: 0.8741 (tp30) cc_final: 0.8516 (tp30) REVERT: A 364 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6132 (pt0) REVERT: B 21 PHE cc_start: 0.8546 (m-80) cc_final: 0.8294 (m-80) REVERT: B 61 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7807 (mmtp) REVERT: B 89 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8187 (t) REVERT: B 117 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6787 (mm-30) REVERT: B 118 LYS cc_start: 0.7752 (tptt) cc_final: 0.7443 (tptt) REVERT: B 205 GLU cc_start: 0.7438 (mp0) cc_final: 0.6970 (mp0) REVERT: B 207 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 215 LYS cc_start: 0.8453 (mttp) cc_final: 0.8185 (mtmm) REVERT: C 44 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.7023 (mpp) REVERT: C 72 GLU cc_start: 0.7692 (tt0) cc_final: 0.7398 (tp30) REVERT: C 99 GLU cc_start: 0.7567 (pm20) cc_final: 0.7268 (pm20) REVERT: C 113 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8118 (mtmm) REVERT: C 118 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8186 (mttm) REVERT: C 297 ASN cc_start: 0.8556 (m110) cc_final: 0.8267 (m110) REVERT: C 334 GLU cc_start: 0.7735 (pm20) cc_final: 0.7482 (pm20) REVERT: D 90 PHE cc_start: 0.8342 (m-80) cc_final: 0.7782 (m-80) REVERT: D 99 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: D 132 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7905 (ppp) REVERT: D 180 LEU cc_start: 0.8929 (tp) cc_final: 0.8718 (tt) REVERT: D 211 ASP cc_start: 0.8123 (t0) cc_final: 0.7882 (t0) REVERT: D 284 LYS cc_start: 0.8554 (mttp) cc_final: 0.8249 (mtpm) REVERT: D 305 MET cc_start: 0.8886 (mmp) cc_final: 0.8662 (mmm) REVERT: E 99 GLU cc_start: 0.7613 (pm20) cc_final: 0.7407 (pp20) REVERT: E 205 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7428 (mt-10) REVERT: E 288 ASP cc_start: 0.7786 (m-30) cc_final: 0.7481 (m-30) REVERT: E 313 MET cc_start: 0.8457 (mmm) cc_final: 0.8230 (mmm) REVERT: F 99 GLU cc_start: 0.7745 (mp0) cc_final: 0.7359 (mp0) REVERT: F 113 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7672 (mmtp) REVERT: F 210 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8034 (ttm110) REVERT: F 241 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: F 314 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: F 354 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7222 (mm-40) REVERT: G 116 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7592 (ttm-80) REVERT: G 125 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: G 147 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8365 (ptm160) REVERT: G 270 GLU cc_start: 0.6466 (mp0) cc_final: 0.4926 (tt0) REVERT: G 276 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7791 (mt-10) outliers start: 94 outliers final: 51 residues processed: 641 average time/residue: 1.5126 time to fit residues: 1072.1116 Evaluate side-chains 651 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 587 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 47 optimal weight: 0.0970 chunk 156 optimal weight: 0.7980 chunk 168 optimal weight: 0.3980 chunk 121 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 12 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN D 12 ASN D 162 ASN D 225 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 78 ASN E 92 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN G 12 ASN G 297 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20815 Z= 0.190 Angle : 0.626 10.650 28254 Z= 0.296 Chirality : 0.046 0.211 3141 Planarity : 0.004 0.065 3609 Dihedral : 9.475 169.515 2933 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.90 % Allowed : 20.93 % Favored : 75.17 % 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: 0.61 (0.17), residues: 2540 helix: 0.45 (0.16), residues: 1110 sheet: 0.63 (0.24), residues: 477 loop : 0.50 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 356 HIS 0.004 0.001 HIS C 161 PHE 0.012 0.001 PHE F 255 TYR 0.021 0.001 TYR A 198 ARG 0.013 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 590 time to evaluate : 2.442 Fit side-chains REVERT: A 61 LYS cc_start: 0.8179 (pttp) cc_final: 0.7774 (pttp) REVERT: A 82 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7347 (tpp) REVERT: A 99 GLU cc_start: 0.7560 (mp0) cc_final: 0.7218 (mp0) REVERT: A 265 SER cc_start: 0.8763 (m) cc_final: 0.8430 (t) REVERT: A 299 MET cc_start: 0.8532 (mtp) cc_final: 0.8182 (mtm) REVERT: A 316 GLU cc_start: 0.8738 (tp30) cc_final: 0.8340 (tp30) REVERT: B 21 PHE cc_start: 0.8544 (m-80) cc_final: 0.8281 (m-80) REVERT: B 61 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7813 (mmtp) REVERT: B 89 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8138 (t) REVERT: B 117 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6801 (mm-30) REVERT: B 118 LYS cc_start: 0.7785 (tptt) cc_final: 0.7460 (tptt) REVERT: B 205 GLU cc_start: 0.7431 (mp0) cc_final: 0.6961 (mp0) REVERT: B 207 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7759 (mm-30) REVERT: C 44 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7051 (mpp) REVERT: C 72 GLU cc_start: 0.7688 (tt0) cc_final: 0.7393 (tp30) REVERT: C 99 GLU cc_start: 0.7566 (pm20) cc_final: 0.7269 (pm20) REVERT: C 113 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8093 (mtmm) REVERT: C 118 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8200 (mttm) REVERT: C 148 THR cc_start: 0.8600 (m) cc_final: 0.8296 (t) REVERT: C 297 ASN cc_start: 0.8545 (m110) cc_final: 0.8266 (m110) REVERT: C 334 GLU cc_start: 0.7722 (pm20) cc_final: 0.7481 (pm20) REVERT: D 90 PHE cc_start: 0.8355 (m-80) cc_final: 0.7819 (m-80) REVERT: D 99 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: D 132 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7975 (ppp) REVERT: D 180 LEU cc_start: 0.8918 (tp) cc_final: 0.8709 (tt) REVERT: D 211 ASP cc_start: 0.8124 (t0) cc_final: 0.7893 (t0) REVERT: D 284 LYS cc_start: 0.8531 (mttp) cc_final: 0.8231 (mtpm) REVERT: D 305 MET cc_start: 0.8892 (mmp) cc_final: 0.8659 (mmm) REVERT: E 115 ASN cc_start: 0.8041 (t0) cc_final: 0.7796 (t0) REVERT: E 202 THR cc_start: 0.8524 (p) cc_final: 0.8172 (p) REVERT: E 288 ASP cc_start: 0.7786 (m-30) cc_final: 0.7484 (m-30) REVERT: E 313 MET cc_start: 0.8453 (mmm) cc_final: 0.8198 (tpt) REVERT: F 99 GLU cc_start: 0.7737 (mp0) cc_final: 0.7369 (mp0) REVERT: F 113 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7676 (mmtp) REVERT: F 210 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8051 (ttm110) REVERT: F 241 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: F 314 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: F 327 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8346 (mp) REVERT: F 354 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7254 (mm-40) REVERT: G 9 VAL cc_start: 0.8402 (t) cc_final: 0.8126 (m) REVERT: G 99 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: G 116 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7569 (ttm-80) REVERT: G 125 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: G 147 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8310 (ptm160) REVERT: G 270 GLU cc_start: 0.6395 (mp0) cc_final: 0.4870 (tt0) REVERT: G 276 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7799 (mt-10) outliers start: 85 outliers final: 57 residues processed: 624 average time/residue: 1.7032 time to fit residues: 1193.3947 Evaluate side-chains 666 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 594 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.5980 chunk 236 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 217 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 12 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN C 353 GLN D 12 ASN D 115 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 297 ASN D 371 HIS E 59 GLN E 78 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 246 GLN G 12 ASN G 115 ASN G 162 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20815 Z= 0.314 Angle : 0.678 10.628 28254 Z= 0.324 Chirality : 0.048 0.213 3141 Planarity : 0.005 0.065 3609 Dihedral : 9.583 162.756 2930 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.76 % Allowed : 21.39 % Favored : 74.85 % 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: 0.50 (0.17), residues: 2540 helix: 0.34 (0.16), residues: 1110 sheet: 0.68 (0.24), residues: 468 loop : 0.41 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.005 0.001 HIS C 101 PHE 0.012 0.001 PHE F 31 TYR 0.021 0.001 TYR A 198 ARG 0.012 0.001 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 599 time to evaluate : 2.373 Fit side-chains REVERT: A 61 LYS cc_start: 0.8190 (pttp) cc_final: 0.7742 (pttp) REVERT: A 82 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7387 (tpp) REVERT: A 124 PHE cc_start: 0.8076 (m-10) cc_final: 0.7761 (m-80) REVERT: A 223 PHE cc_start: 0.8064 (t80) cc_final: 0.7792 (t80) REVERT: A 265 SER cc_start: 0.8774 (m) cc_final: 0.8438 (t) REVERT: A 299 MET cc_start: 0.8542 (mtp) cc_final: 0.8202 (mtm) REVERT: A 316 GLU cc_start: 0.8749 (tp30) cc_final: 0.8391 (tp30) REVERT: A 352 PHE cc_start: 0.8101 (t80) cc_final: 0.7786 (t80) REVERT: A 361 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 21 PHE cc_start: 0.8557 (m-80) cc_final: 0.8297 (m-80) REVERT: B 61 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7803 (mmtp) REVERT: B 89 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8216 (t) REVERT: B 117 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6797 (mm-30) REVERT: B 118 LYS cc_start: 0.7807 (tptt) cc_final: 0.7485 (tptt) REVERT: B 205 GLU cc_start: 0.7454 (mp0) cc_final: 0.6980 (mp0) REVERT: B 207 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7792 (mm-30) REVERT: B 211 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7721 (t70) REVERT: C 44 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7075 (mpp) REVERT: C 72 GLU cc_start: 0.7697 (tt0) cc_final: 0.7411 (tp30) REVERT: C 99 GLU cc_start: 0.7566 (pm20) cc_final: 0.7261 (pm20) REVERT: C 113 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8177 (mtmm) REVERT: C 118 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8203 (mttm) REVERT: C 297 ASN cc_start: 0.8553 (m110) cc_final: 0.8281 (m110) REVERT: C 334 GLU cc_start: 0.7733 (pm20) cc_final: 0.7491 (pm20) REVERT: D 107 GLU cc_start: 0.7690 (tp30) cc_final: 0.7369 (mm-30) REVERT: D 132 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7919 (ppp) REVERT: D 180 LEU cc_start: 0.8951 (tp) cc_final: 0.8730 (tt) REVERT: D 211 ASP cc_start: 0.8126 (t0) cc_final: 0.7912 (t0) REVERT: D 284 LYS cc_start: 0.8562 (mttp) cc_final: 0.8262 (mtpm) REVERT: D 305 MET cc_start: 0.8962 (mmp) cc_final: 0.8696 (mmm) REVERT: E 288 ASP cc_start: 0.7718 (m-30) cc_final: 0.7409 (m-30) REVERT: E 313 MET cc_start: 0.8458 (mmm) cc_final: 0.8254 (mmm) REVERT: F 99 GLU cc_start: 0.7754 (mp0) cc_final: 0.7394 (mp0) REVERT: F 113 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7784 (mmtp) REVERT: F 210 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8070 (ttm110) REVERT: F 222 ASP cc_start: 0.7840 (t0) cc_final: 0.7586 (t0) REVERT: F 241 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: F 314 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: F 354 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7265 (mm-40) REVERT: G 9 VAL cc_start: 0.8408 (t) cc_final: 0.8104 (m) REVERT: G 99 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: G 116 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7562 (ttm-80) REVERT: G 125 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: G 147 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8370 (ptm160) REVERT: G 270 GLU cc_start: 0.6467 (mp0) cc_final: 0.4881 (tt0) REVERT: G 276 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7805 (mt-10) outliers start: 82 outliers final: 51 residues processed: 635 average time/residue: 1.6093 time to fit residues: 1129.7979 Evaluate side-chains 667 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 602 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 99 GLU Chi-restraints excluded: chain G residue 116 ARG Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain G residue 359 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 169 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN C 353 GLN D 12 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN F 59 GLN F 137 GLN F 246 GLN G 12 ASN G 162 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20815 Z= 0.301 Angle : 0.684 10.834 28254 Z= 0.327 Chirality : 0.048 0.209 3141 Planarity : 0.005 0.068 3609 Dihedral : 9.499 156.843 2927 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.49 % Allowed : 22.07 % Favored : 74.44 % 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: 0.46 (0.17), residues: 2540 helix: 0.30 (0.16), residues: 1110 sheet: 0.58 (0.24), residues: 468 loop : 0.43 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.005 0.001 HIS C 161 PHE 0.012 0.001 PHE F 255 TYR 0.018 0.001 TYR A 198 ARG 0.012 0.001 ARG F 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 596 time to evaluate : 2.340 Fit side-chains REVERT: A 61 LYS cc_start: 0.8180 (pttp) cc_final: 0.7709 (pttp) REVERT: A 81 ASP cc_start: 0.7832 (p0) cc_final: 0.7531 (p0) REVERT: A 82 MET cc_start: 0.7691 (mmp) cc_final: 0.7262 (tpp) REVERT: A 124 PHE cc_start: 0.8071 (m-10) cc_final: 0.7789 (m-80) REVERT: A 223 PHE cc_start: 0.8087 (t80) cc_final: 0.7637 (t80) REVERT: A 226 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: A 265 SER cc_start: 0.8790 (m) cc_final: 0.8461 (t) REVERT: A 299 MET cc_start: 0.8550 (mtp) cc_final: 0.8217 (mtm) REVERT: A 316 GLU cc_start: 0.8750 (tp30) cc_final: 0.8382 (tp30) REVERT: A 352 PHE cc_start: 0.8132 (t80) cc_final: 0.7785 (t80) REVERT: A 359 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7717 (mmmm) REVERT: A 361 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 21 PHE cc_start: 0.8551 (m-80) cc_final: 0.8329 (m-80) REVERT: B 28 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7805 (ttm170) REVERT: B 61 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7800 (mmtp) REVERT: B 89 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8199 (t) REVERT: B 117 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6783 (mm-30) REVERT: B 118 LYS cc_start: 0.7774 (tptt) cc_final: 0.7468 (tptt) REVERT: B 205 GLU cc_start: 0.7456 (mp0) cc_final: 0.6959 (mp0) REVERT: B 207 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7776 (mm-30) REVERT: B 211 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7688 (t70) REVERT: B 241 GLU cc_start: 0.7412 (tp30) cc_final: 0.6808 (tp30) REVERT: C 44 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7098 (mpp) REVERT: C 72 GLU cc_start: 0.7707 (tt0) cc_final: 0.7411 (tp30) REVERT: C 99 GLU cc_start: 0.7568 (pm20) cc_final: 0.7264 (pm20) REVERT: C 113 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8175 (mtmm) REVERT: C 118 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8202 (mttm) REVERT: C 153 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8516 (tp) REVERT: C 297 ASN cc_start: 0.8557 (m110) cc_final: 0.8250 (m110) REVERT: C 334 GLU cc_start: 0.7714 (pm20) cc_final: 0.7473 (pm20) REVERT: D 90 PHE cc_start: 0.8335 (m-80) cc_final: 0.7815 (m-80) REVERT: D 132 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7914 (ppp) REVERT: D 180 LEU cc_start: 0.8948 (tp) cc_final: 0.8733 (tt) REVERT: D 211 ASP cc_start: 0.8130 (t0) cc_final: 0.7915 (t0) REVERT: D 284 LYS cc_start: 0.8564 (mttp) cc_final: 0.8333 (mttm) REVERT: D 305 MET cc_start: 0.8981 (mmp) cc_final: 0.8723 (mmm) REVERT: E 288 ASP cc_start: 0.7713 (m-30) cc_final: 0.7400 (m-30) REVERT: F 99 GLU cc_start: 0.7754 (mp0) cc_final: 0.7388 (mp0) REVERT: F 113 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7678 (mmtp) REVERT: F 210 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8036 (ttm110) REVERT: F 241 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: F 314 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: F 354 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7234 (mm-40) REVERT: G 125 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: G 147 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8320 (ptm160) REVERT: G 270 GLU cc_start: 0.6455 (mp0) cc_final: 0.4887 (tt0) REVERT: G 276 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7795 (mt-10) outliers start: 76 outliers final: 49 residues processed: 628 average time/residue: 1.6345 time to fit residues: 1134.1473 Evaluate side-chains 675 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 612 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 121 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 187 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 208 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 111 ASN A 115 ASN B 111 ASN B 297 ASN C 137 GLN C 162 ASN C 353 GLN D 162 ASN D 225 ASN E 59 GLN E 78 ASN E 115 ASN E 225 ASN E 353 GLN F 59 GLN F 137 GLN F 246 GLN G 12 ASN G 162 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091982 restraints weight = 29726.691| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.63 r_work: 0.3009 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20815 Z= 0.235 Angle : 0.674 12.928 28254 Z= 0.319 Chirality : 0.047 0.235 3141 Planarity : 0.005 0.068 3609 Dihedral : 9.335 153.165 2927 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.12 % Allowed : 22.53 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2540 helix: 0.38 (0.16), residues: 1109 sheet: 0.55 (0.24), residues: 481 loop : 0.50 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.005 0.001 HIS C 161 PHE 0.012 0.001 PHE F 255 TYR 0.019 0.001 TYR A 198 ARG 0.013 0.001 ARG F 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14234.76 seconds wall clock time: 345 minutes 23.93 seconds (20723.93 seconds total)