Starting phenix.real_space_refine on Tue Nov 19 02:02:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/11_2024/8gyk_34372.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/11_2024/8gyk_34372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/11_2024/8gyk_34372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/11_2024/8gyk_34372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/11_2024/8gyk_34372.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyk_34372/11_2024/8gyk_34372.cif" } resolution = 3.14 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= 0.004 sd= 0.073 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 16 5.49 5 Mg 8 5.21 5 S 96 5.16 5 C 11290 2.51 5 N 3211 2.21 5 O 3482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18103 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2233 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2249 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain breaks: 2 Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2241 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 2 Chain: "D" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2225 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 6, 'TRANS': 282} Chain breaks: 2 Chain: "E" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2232 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2233 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain breaks: 2 Chain: "G" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2241 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 2 Chain: "H" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2225 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 6, 'TRANS': 282} Chain breaks: 2 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} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.55, per 1000 atoms: 0.64 Number of scatterers: 18103 At special positions: 0 Unit cell: (124.5, 122.84, 146.08, 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 96 16.00 P 16 15.00 Mg 8 11.99 O 3482 8.00 N 3211 7.00 C 11290 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: 4.46 Conformation dependent library (CDL) restraints added in 2.1 seconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 14 sheets defined 50.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.821A pdb=" N GLU A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.636A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.508A pdb=" N ASP A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.605A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.570A pdb=" N ASP A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.909A pdb=" N GLU B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 45 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.514A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 80 Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.646A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 197 through 214 removed outlier: 3.793A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.584A pdb=" N TYR B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.916A pdb=" N HIS B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.933A pdb=" N GLU C 29 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.724A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.653A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 189 removed outlier: 3.698A pdb=" N LEU C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.711A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.551A pdb=" N ARG D 27 " --> pdb=" O PRO D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.832A pdb=" N GLU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.709A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 88 through 97 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.531A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.669A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 189 removed outlier: 3.628A pdb=" N ASN D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.820A pdb=" N THR D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 removed outlier: 3.507A pdb=" N THR D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'E' and resid 24 through 29 Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 removed outlier: 3.794A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 removed outlier: 3.612A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.577A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 178 removed outlier: 4.065A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.703A pdb=" N VAL E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.623A pdb=" N THR E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 3.566A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 260 removed outlier: 4.490A pdb=" N GLU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.817A pdb=" N GLU F 29 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 43 removed outlier: 3.741A pdb=" N LYS F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 62 removed outlier: 3.521A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.691A pdb=" N LYS F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.512A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.848A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 187 removed outlier: 3.819A pdb=" N LEU F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 214 removed outlier: 3.855A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 removed outlier: 3.608A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 260 removed outlier: 3.606A pdb=" N MET F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.536A pdb=" N GLU G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 43 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 62 Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 178 removed outlier: 3.836A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR G 178 " --> pdb=" O VAL G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 189 removed outlier: 3.516A pdb=" N VAL G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 189 " --> pdb=" O VAL G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 214 removed outlier: 3.973A pdb=" N THR G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 231 removed outlier: 3.503A pdb=" N ASP G 231 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 removed outlier: 3.758A pdb=" N PHE G 259 " --> pdb=" O LEU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 296 removed outlier: 3.716A pdb=" N HIS G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA G 295 " --> pdb=" O ILE G 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 34 through 43 removed outlier: 3.752A pdb=" N GLU H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.512A pdb=" N LEU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 97 Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 167 through 178 removed outlier: 3.647A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 172 " --> pdb=" O PRO H 168 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 178 " --> pdb=" O VAL H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 189 removed outlier: 3.673A pdb=" N ASN H 188 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL H 189 " --> pdb=" O VAL H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 211 removed outlier: 3.809A pdb=" N THR H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 232 removed outlier: 3.594A pdb=" N THR H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 260 removed outlier: 3.838A pdb=" N MET H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS H 244 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 125 removed outlier: 3.648A pdb=" N ILE A 265 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'B' and resid 301 through 306 removed outlier: 3.567A pdb=" N ILE B 311 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY B 305 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N THR B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.309A pdb=" N MET D 158 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 122 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU D 300 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU D 124 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU D 302 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 311 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY D 305 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 264 through 266 removed outlier: 6.133A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.502A pdb=" N ILE C 311 " --> pdb=" O ARG C 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.667A pdb=" N MET F 158 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE F 327 " --> pdb=" O ARG F 310 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS F 312 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 190 through 191 removed outlier: 6.873A pdb=" N ALA E 157 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS E 156 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU E 219 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET E 158 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA E 217 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL E 264 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU E 219 " --> pdb=" O VAL E 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AB3, first strand: chain 'G' and resid 87 through 88 removed outlier: 6.294A pdb=" N MET H 158 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR H 266 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE H 122 " --> pdb=" O THR H 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 264 through 266 removed outlier: 6.158A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE G 126 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG G 303 " --> pdb=" O ILE G 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 311 " --> pdb=" O ARG G 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 301 through 303 727 hydrogen bonds defined for protein. 2049 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: 5.45 Time building geometry restraints manager: 5.15 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: 6086 1.34 - 1.46: 3112 1.46 - 1.58: 8960 1.58 - 1.69: 25 1.69 - 1.81: 160 Bond restraints: 18343 Sorted by residual: bond pdb=" CG PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 1.503 1.286 0.217 3.40e-02 8.65e+02 4.06e+01 bond pdb=" CB PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 1.492 1.688 -0.196 5.00e-02 4.00e+02 1.53e+01 bond pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 9.02e+00 bond pdb=" N PRO C 83 " pdb=" CA PRO C 83 " ideal model delta sigma weight residual 1.469 1.450 0.019 1.28e-02 6.10e+03 2.22e+00 bond pdb=" C4 ADP B 600 " pdb=" C5 ADP B 600 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 18338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 24505 3.10 - 6.21: 225 6.21 - 9.31: 12 9.31 - 12.42: 2 12.42 - 15.52: 2 Bond angle restraints: 24746 Sorted by residual: angle pdb=" CA PRO C 83 " pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 112.00 96.48 15.52 1.40e+00 5.10e-01 1.23e+02 angle pdb=" N PRO C 83 " pdb=" CD PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 103.20 89.22 13.98 1.50e+00 4.44e-01 8.69e+01 angle pdb=" CA PRO C 83 " pdb=" CB PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 104.50 93.55 10.95 1.90e+00 2.77e-01 3.32e+01 angle pdb=" N ILE A 314 " pdb=" CA ILE A 314 " pdb=" C ILE A 314 " ideal model delta sigma weight residual 113.10 107.75 5.35 9.70e-01 1.06e+00 3.04e+01 angle pdb=" N MET H 326 " pdb=" CA MET H 326 " pdb=" C MET H 326 " ideal model delta sigma weight residual 109.85 115.92 -6.07 1.58e+00 4.01e-01 1.48e+01 ... (remaining 24741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 10579 28.42 - 56.84: 419 56.84 - 85.25: 45 85.25 - 113.67: 8 113.67 - 142.09: 13 Dihedral angle restraints: 11064 sinusoidal: 4445 harmonic: 6619 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 82.09 -142.09 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O1B ADP B 600 " pdb=" O3A ADP B 600 " pdb=" PB ADP B 600 " pdb=" PA ADP B 600 " ideal model delta sinusoidal sigma weight residual 300.00 162.60 137.40 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' ADP B 600 " pdb=" O5' ADP B 600 " pdb=" PA ADP B 600 " pdb=" O2A ADP B 600 " ideal model delta sinusoidal sigma weight residual -60.00 76.96 -136.96 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2213 0.046 - 0.092: 477 0.092 - 0.138: 141 0.138 - 0.184: 8 0.184 - 0.230: 1 Chirality restraints: 2840 Sorted by residual: chirality pdb=" CB ILE G 314 " pdb=" CA ILE G 314 " pdb=" CG1 ILE G 314 " pdb=" CG2 ILE G 314 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE C 314 " pdb=" CA ILE C 314 " pdb=" CG1 ILE C 314 " pdb=" CG2 ILE C 314 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CB ILE E 314 " pdb=" CA ILE E 314 " pdb=" CG1 ILE E 314 " pdb=" CG2 ILE E 314 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 2837 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 82 " 0.061 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO C 83 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 23 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO F 24 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 24 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 24 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 21 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO B 22 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.034 5.00e-02 4.00e+02 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 221 2.58 - 3.16: 15718 3.16 - 3.74: 28301 3.74 - 4.32: 38684 4.32 - 4.90: 63197 Nonbonded interactions: 146121 Sorted by model distance: nonbonded pdb=" O2A ADP G 600 " pdb="MG MG G 601 " model vdw 2.003 2.170 nonbonded pdb=" O1A ADP E 600 " pdb="MG MG E 601 " model vdw 2.004 2.170 nonbonded pdb=" O3B ADP B 600 " pdb="MG MG B 601 " model vdw 2.016 2.170 nonbonded pdb=" O3A ADP H 600 " pdb="MG MG H 601 " model vdw 2.025 2.170 nonbonded pdb=" O3A ADP B 600 " pdb="MG MG B 601 " model vdw 2.030 2.170 ... (remaining 146116 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' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'B' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'C' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'D' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 336 or resid 600 through 601)) selection = (chain 'E' and (resid 21 through 270 or resid 291 through 336 or resid 600 throu \ gh 601)) selection = (chain 'F' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'G' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 270 or resid 291 through 336 or \ resid 600 through 601)) selection = (chain 'H' and (resid 21 through 232 or (resid 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 through 336 or resid 600 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.100 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 : 0.003 0.217 18343 Z= 0.223 Angle : 0.733 15.524 24746 Z= 0.383 Chirality : 0.042 0.230 2840 Planarity : 0.005 0.082 3163 Dihedral : 15.842 142.089 6826 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.41 % Favored : 92.89 % Rotamer: Outliers : 0.05 % Allowed : 0.22 % Favored : 99.73 % 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: -2.07 (0.17), residues: 2277 helix: -0.62 (0.16), residues: 1067 sheet: -1.65 (0.31), residues: 309 loop : -2.09 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 244 PHE 0.020 0.001 PHE A 126 TYR 0.022 0.001 TYR C 315 ARG 0.014 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7678 (p) cc_final: 0.7352 (t) REVERT: B 50 GLU cc_start: 0.6821 (mt-10) cc_final: 0.5237 (pt0) REVERT: B 253 LEU cc_start: 0.7411 (mm) cc_final: 0.7060 (mt) REVERT: B 313 LYS cc_start: 0.6027 (mttp) cc_final: 0.5558 (pttp) REVERT: C 97 SER cc_start: 0.6994 (m) cc_final: 0.6657 (p) REVERT: C 111 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7670 (mttm) REVERT: C 118 GLU cc_start: 0.7204 (pt0) cc_final: 0.6915 (tt0) REVERT: C 124 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6970 (tt0) REVERT: C 126 PHE cc_start: 0.7481 (m-10) cc_final: 0.6978 (m-80) REVERT: C 242 GLN cc_start: 0.8005 (mm110) cc_final: 0.7525 (mm-40) REVERT: C 250 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7317 (mtp-110) REVERT: C 255 LEU cc_start: 0.7774 (tt) cc_final: 0.7572 (tp) REVERT: C 315 TYR cc_start: 0.7331 (t80) cc_final: 0.6962 (t80) REVERT: D 97 SER cc_start: 0.7961 (t) cc_final: 0.7711 (p) REVERT: D 170 ARG cc_start: 0.7558 (tpp-160) cc_final: 0.7247 (tpp80) REVERT: D 178 TYR cc_start: 0.8020 (m-10) cc_final: 0.7812 (m-10) REVERT: D 208 SER cc_start: 0.8620 (t) cc_final: 0.8362 (t) REVERT: D 267 ASN cc_start: 0.7747 (t0) cc_final: 0.7542 (t0) REVERT: D 326 MET cc_start: 0.6806 (mmp) cc_final: 0.6589 (tmm) REVERT: E 140 LEU cc_start: 0.7384 (tp) cc_final: 0.6726 (mt) REVERT: F 124 GLU cc_start: 0.7391 (tt0) cc_final: 0.6950 (tt0) REVERT: F 301 TYR cc_start: 0.7670 (t80) cc_final: 0.7279 (t80) REVERT: G 68 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7317 (mm-30) REVERT: G 126 PHE cc_start: 0.6690 (m-80) cc_final: 0.5868 (m-10) REVERT: G 130 ARG cc_start: 0.6596 (mtt90) cc_final: 0.6177 (mmm160) REVERT: G 154 GLU cc_start: 0.7181 (pt0) cc_final: 0.6339 (tp30) REVERT: G 326 MET cc_start: 0.5126 (mmp) cc_final: 0.4495 (mmp) REVERT: H 210 MET cc_start: 0.8613 (ptm) cc_final: 0.8276 (ptp) REVERT: H 250 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7162 (ttp-110) REVERT: H 267 ASN cc_start: 0.7491 (t0) cc_final: 0.7143 (t0) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.3645 time to fit residues: 244.9440 Evaluate side-chains 322 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 244 HIS B 23 GLN B 101 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 330 ASN D 62 ASN D 206 GLN E 188 ASN E 206 GLN F 135 GLN G 135 GLN H 200 GLN H 294 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18343 Z= 0.247 Angle : 0.730 7.712 24746 Z= 0.353 Chirality : 0.045 0.212 2840 Planarity : 0.005 0.059 3163 Dihedral : 10.134 130.726 2629 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.68 % Favored : 92.67 % Rotamer: Outliers : 1.62 % Allowed : 10.57 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2277 helix: -0.36 (0.15), residues: 1087 sheet: -1.90 (0.28), residues: 330 loop : -2.11 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 47 PHE 0.030 0.002 PHE A 327 TYR 0.017 0.002 TYR E 315 ARG 0.009 0.001 ARG H 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 341 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7846 (p) cc_final: 0.7573 (t) REVERT: A 211 MET cc_start: 0.6460 (mmt) cc_final: 0.6257 (tpp) REVERT: A 229 ARG cc_start: 0.5115 (mmt180) cc_final: 0.4881 (mmt180) REVERT: B 84 MET cc_start: 0.7968 (mtp) cc_final: 0.7708 (mmm) REVERT: B 130 ARG cc_start: 0.7113 (mmp-170) cc_final: 0.6476 (mtp85) REVERT: B 229 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7527 (mtt90) REVERT: C 80 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8279 (mtmm) REVERT: C 163 GLU cc_start: 0.6537 (tp30) cc_final: 0.5752 (tp30) REVERT: C 187 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7146 (t0) REVERT: C 205 TYR cc_start: 0.8455 (m-10) cc_final: 0.8176 (m-10) REVERT: C 242 GLN cc_start: 0.8046 (mm110) cc_final: 0.7527 (mm-40) REVERT: C 250 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7309 (mtp-110) REVERT: C 267 ASN cc_start: 0.8038 (t0) cc_final: 0.7822 (t0) REVERT: D 95 ARG cc_start: 0.6893 (ptt90) cc_final: 0.6405 (mmp80) REVERT: D 170 ARG cc_start: 0.7742 (tpp-160) cc_final: 0.7462 (mmm-85) REVERT: D 208 SER cc_start: 0.8501 (t) cc_final: 0.8225 (t) REVERT: D 243 MET cc_start: 0.7422 (tmm) cc_final: 0.7095 (tmm) REVERT: D 250 ARG cc_start: 0.7600 (tpt170) cc_final: 0.7245 (ttm110) REVERT: D 315 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.5685 (m-80) REVERT: D 326 MET cc_start: 0.6690 (mmp) cc_final: 0.6349 (tmm) REVERT: E 251 MET cc_start: 0.7505 (mtm) cc_final: 0.7294 (tpt) REVERT: F 251 MET cc_start: 0.7285 (mtp) cc_final: 0.6956 (mtp) REVERT: G 59 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6913 (mt-10) REVERT: G 68 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7483 (tp30) REVERT: G 130 ARG cc_start: 0.6800 (mtt90) cc_final: 0.6299 (mmm160) REVERT: G 205 TYR cc_start: 0.7679 (m-10) cc_final: 0.7432 (m-10) REVERT: G 210 MET cc_start: 0.8498 (mtm) cc_final: 0.8289 (mtp) REVERT: G 219 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8373 (tt) REVERT: G 326 MET cc_start: 0.5177 (mmp) cc_final: 0.4302 (mtm) REVERT: H 100 ILE cc_start: 0.7368 (mm) cc_final: 0.6964 (mm) REVERT: H 118 GLU cc_start: 0.7415 (tt0) cc_final: 0.6886 (pt0) REVERT: H 128 GLU cc_start: 0.6316 (tp30) cc_final: 0.6090 (tp30) REVERT: H 148 ILE cc_start: 0.7609 (tp) cc_final: 0.7399 (tp) REVERT: H 170 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.7136 (tpt90) REVERT: H 250 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.7110 (ttp-110) REVERT: H 257 ASP cc_start: 0.7475 (t70) cc_final: 0.7208 (t0) REVERT: H 267 ASN cc_start: 0.7658 (t0) cc_final: 0.7245 (t0) outliers start: 30 outliers final: 15 residues processed: 356 average time/residue: 0.3405 time to fit residues: 177.9818 Evaluate side-chains 308 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 290 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 23 GLN C 135 GLN C 330 ASN D 196 ASN D 200 GLN E 188 ASN E 206 GLN F 135 GLN ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN H 200 GLN H 206 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18343 Z= 0.323 Angle : 0.724 8.415 24746 Z= 0.349 Chirality : 0.045 0.218 2840 Planarity : 0.004 0.055 3163 Dihedral : 9.654 132.993 2629 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.29 % Favored : 92.05 % Rotamer: Outliers : 2.64 % Allowed : 15.05 % Favored : 82.31 % 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: -1.93 (0.17), residues: 2277 helix: -0.28 (0.15), residues: 1102 sheet: -2.02 (0.29), residues: 290 loop : -2.22 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS A 294 PHE 0.026 0.002 PHE A 327 TYR 0.023 0.002 TYR H 159 ARG 0.012 0.001 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 359 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7887 (p) cc_final: 0.7559 (t) REVERT: B 39 LYS cc_start: 0.7483 (mtmm) cc_final: 0.6747 (ttpp) REVERT: B 84 MET cc_start: 0.7976 (mtp) cc_final: 0.7572 (mmm) REVERT: B 130 ARG cc_start: 0.7286 (mmp-170) cc_final: 0.6592 (mtp85) REVERT: B 313 LYS cc_start: 0.6277 (mttp) cc_final: 0.5909 (pttp) REVERT: B 326 MET cc_start: 0.7170 (tpp) cc_final: 0.6832 (mmt) REVERT: C 205 TYR cc_start: 0.8493 (m-10) cc_final: 0.8170 (m-10) REVERT: C 242 GLN cc_start: 0.8096 (mm110) cc_final: 0.7544 (mm-40) REVERT: C 243 MET cc_start: 0.6930 (mmt) cc_final: 0.6642 (mpp) REVERT: C 250 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7297 (mtp-110) REVERT: C 267 ASN cc_start: 0.8237 (t0) cc_final: 0.8027 (t0) REVERT: C 315 TYR cc_start: 0.7193 (t80) cc_final: 0.6833 (t80) REVERT: D 95 ARG cc_start: 0.6876 (ptt90) cc_final: 0.6446 (mmp80) REVERT: D 170 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7280 (tpp80) REVERT: D 315 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5662 (m-80) REVERT: D 326 MET cc_start: 0.6941 (mmp) cc_final: 0.6642 (tmm) REVERT: D 332 ASP cc_start: 0.8324 (p0) cc_final: 0.7966 (p0) REVERT: E 210 MET cc_start: 0.8566 (ptm) cc_final: 0.8325 (ptp) REVERT: E 250 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6728 (tpp-160) REVERT: E 251 MET cc_start: 0.7533 (mtm) cc_final: 0.7304 (tpp) REVERT: F 64 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7621 (mtpp) REVERT: F 251 MET cc_start: 0.7266 (mtp) cc_final: 0.6899 (mtp) REVERT: G 118 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7029 (pt0) REVERT: G 130 ARG cc_start: 0.7067 (mtt90) cc_final: 0.6505 (mmm160) REVERT: G 205 TYR cc_start: 0.7858 (m-10) cc_final: 0.7396 (m-10) REVERT: G 210 MET cc_start: 0.8539 (mtm) cc_final: 0.8198 (mtp) REVERT: G 219 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8450 (tt) REVERT: G 326 MET cc_start: 0.5741 (mmp) cc_final: 0.4859 (mtm) REVERT: H 100 ILE cc_start: 0.7601 (mm) cc_final: 0.7149 (mm) REVERT: H 118 GLU cc_start: 0.7498 (tt0) cc_final: 0.6916 (pt0) REVERT: H 250 ARG cc_start: 0.7410 (ttp-110) cc_final: 0.7154 (ttp-110) outliers start: 49 outliers final: 28 residues processed: 380 average time/residue: 0.3391 time to fit residues: 188.1520 Evaluate side-chains 338 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 210 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 206 GLN C 330 ASN D 200 GLN E 206 GLN F 268 GLN ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18343 Z= 0.252 Angle : 0.686 7.879 24746 Z= 0.326 Chirality : 0.043 0.170 2840 Planarity : 0.004 0.063 3163 Dihedral : 9.092 129.714 2629 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.90 % Favored : 92.45 % Rotamer: Outliers : 3.24 % Allowed : 16.50 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.17), residues: 2277 helix: -0.08 (0.16), residues: 1090 sheet: -2.04 (0.29), residues: 288 loop : -2.14 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 294 PHE 0.025 0.002 PHE A 327 TYR 0.020 0.001 TYR E 315 ARG 0.003 0.000 ARG E 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 316 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7836 (p) cc_final: 0.7524 (t) REVERT: B 84 MET cc_start: 0.7977 (mtp) cc_final: 0.7642 (mmm) REVERT: B 130 ARG cc_start: 0.7230 (mmp-170) cc_final: 0.6561 (mtp85) REVERT: C 94 GLN cc_start: 0.7052 (pp30) cc_final: 0.6616 (mt0) REVERT: C 242 GLN cc_start: 0.8070 (mm110) cc_final: 0.7515 (mm-40) REVERT: C 243 MET cc_start: 0.6952 (mmt) cc_final: 0.6733 (mpp) REVERT: C 250 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7277 (mtp-110) REVERT: C 267 ASN cc_start: 0.8230 (t0) cc_final: 0.8003 (t0) REVERT: C 315 TYR cc_start: 0.7307 (t80) cc_final: 0.6838 (t80) REVERT: D 170 ARG cc_start: 0.7797 (tpp-160) cc_final: 0.7165 (tpp80) REVERT: D 211 MET cc_start: 0.7607 (mmm) cc_final: 0.7393 (mtp) REVERT: D 249 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7579 (mm) REVERT: D 315 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6097 (m-80) REVERT: D 326 MET cc_start: 0.7028 (mmp) cc_final: 0.6637 (tmm) REVERT: E 23 GLN cc_start: 0.8363 (mt0) cc_final: 0.8136 (mt0) REVERT: E 250 ARG cc_start: 0.7154 (ttp-110) cc_final: 0.6750 (tpp-160) REVERT: F 64 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7687 (mtpp) REVERT: F 251 MET cc_start: 0.7289 (mtp) cc_final: 0.6864 (mtp) REVERT: F 268 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7604 (tp40) REVERT: G 43 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: G 59 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7121 (mt-10) REVERT: G 101 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7472 (tp40) REVERT: G 130 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6638 (mmt180) REVERT: G 210 MET cc_start: 0.8474 (mtm) cc_final: 0.8131 (mtp) REVERT: G 254 ARG cc_start: 0.7504 (ttp80) cc_final: 0.6765 (tmm160) REVERT: G 258 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7405 (mp0) REVERT: G 326 MET cc_start: 0.5818 (mmp) cc_final: 0.5000 (mtm) REVERT: H 100 ILE cc_start: 0.7574 (mm) cc_final: 0.7242 (mm) REVERT: H 118 GLU cc_start: 0.7449 (tt0) cc_final: 0.6876 (pt0) REVERT: H 250 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7156 (ttp-110) outliers start: 60 outliers final: 35 residues processed: 349 average time/residue: 0.3405 time to fit residues: 174.0982 Evaluate side-chains 328 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 189 optimal weight: 0.5980 chunk 153 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 93 HIS C 135 GLN C 330 ASN D 200 GLN E 188 ASN E 244 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18343 Z= 0.269 Angle : 0.684 7.613 24746 Z= 0.326 Chirality : 0.043 0.160 2840 Planarity : 0.004 0.057 3163 Dihedral : 8.702 125.847 2629 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.85 % Favored : 92.53 % Rotamer: Outliers : 3.72 % Allowed : 18.12 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.17), residues: 2277 helix: -0.06 (0.16), residues: 1094 sheet: -2.14 (0.29), residues: 283 loop : -2.16 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 294 PHE 0.025 0.001 PHE A 327 TYR 0.017 0.001 TYR E 315 ARG 0.005 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 311 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7838 (p) cc_final: 0.7543 (t) REVERT: B 84 MET cc_start: 0.7968 (mtp) cc_final: 0.7629 (mmm) REVERT: B 313 LYS cc_start: 0.6521 (mttp) cc_final: 0.6020 (pttp) REVERT: C 94 GLN cc_start: 0.7001 (pp30) cc_final: 0.6550 (mt0) REVERT: C 101 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7221 (tp40) REVERT: C 163 GLU cc_start: 0.6726 (tp30) cc_final: 0.5779 (tp30) REVERT: C 202 GLN cc_start: 0.7442 (mp10) cc_final: 0.7105 (tt0) REVERT: C 242 GLN cc_start: 0.8059 (mm110) cc_final: 0.7484 (mm-40) REVERT: C 243 MET cc_start: 0.6941 (mmt) cc_final: 0.6733 (mpp) REVERT: C 250 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7244 (mtp-110) REVERT: C 267 ASN cc_start: 0.8231 (t0) cc_final: 0.8022 (t0) REVERT: C 315 TYR cc_start: 0.7297 (t80) cc_final: 0.6814 (t80) REVERT: D 170 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.7195 (tpp80) REVERT: D 211 MET cc_start: 0.7669 (mmm) cc_final: 0.7396 (mtt) REVERT: D 315 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6078 (m-80) REVERT: D 326 MET cc_start: 0.6824 (mmp) cc_final: 0.6565 (tmm) REVERT: D 332 ASP cc_start: 0.8311 (p0) cc_final: 0.7978 (p0) REVERT: E 94 GLN cc_start: 0.6771 (mt0) cc_final: 0.6403 (mp10) REVERT: E 250 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6818 (tpp-160) REVERT: F 107 LYS cc_start: 0.5522 (tttm) cc_final: 0.5201 (ttpt) REVERT: G 43 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: G 59 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7166 (mt-10) REVERT: G 130 ARG cc_start: 0.7263 (mtt90) cc_final: 0.6702 (mmm160) REVERT: G 210 MET cc_start: 0.8461 (mtm) cc_final: 0.8072 (mtp) REVERT: G 219 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8368 (tt) REVERT: G 326 MET cc_start: 0.5765 (mmp) cc_final: 0.5186 (mtm) REVERT: H 100 ILE cc_start: 0.7644 (mm) cc_final: 0.7278 (mm) REVERT: H 118 GLU cc_start: 0.7439 (tt0) cc_final: 0.6893 (pt0) REVERT: H 250 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.7159 (ttp-110) outliers start: 69 outliers final: 42 residues processed: 354 average time/residue: 0.3314 time to fit residues: 172.1527 Evaluate side-chains 340 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 222 optimal weight: 0.4980 chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18343 Z= 0.343 Angle : 0.712 8.072 24746 Z= 0.341 Chirality : 0.045 0.186 2840 Planarity : 0.004 0.060 3163 Dihedral : 8.520 125.168 2629 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.77 % Favored : 91.70 % Rotamer: Outliers : 4.05 % Allowed : 17.91 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.17), residues: 2277 helix: -0.11 (0.16), residues: 1086 sheet: -2.28 (0.30), residues: 280 loop : -2.21 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 294 PHE 0.025 0.002 PHE A 327 TYR 0.020 0.002 TYR B 301 ARG 0.005 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 319 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7849 (p) cc_final: 0.7536 (t) REVERT: B 178 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7289 (m-10) REVERT: B 229 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7387 (mtt90) REVERT: B 313 LYS cc_start: 0.6533 (mttp) cc_final: 0.6038 (pttp) REVERT: C 94 GLN cc_start: 0.7054 (pp30) cc_final: 0.6591 (mt0) REVERT: C 101 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7283 (tp40) REVERT: C 202 GLN cc_start: 0.7477 (mp10) cc_final: 0.7138 (tt0) REVERT: C 242 GLN cc_start: 0.8060 (mm110) cc_final: 0.7449 (mm-40) REVERT: C 250 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7226 (mtp-110) REVERT: C 315 TYR cc_start: 0.7333 (t80) cc_final: 0.6806 (t80) REVERT: D 170 ARG cc_start: 0.7925 (tpp-160) cc_final: 0.7218 (tpp80) REVERT: D 249 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7547 (mm) REVERT: D 326 MET cc_start: 0.6842 (mmp) cc_final: 0.6639 (tmm) REVERT: D 332 ASP cc_start: 0.8327 (p0) cc_final: 0.7908 (p0) REVERT: E 94 GLN cc_start: 0.6751 (mt0) cc_final: 0.6396 (mp10) REVERT: E 143 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7384 (p) REVERT: F 23 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: F 64 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7605 (mtpp) REVERT: F 107 LYS cc_start: 0.5540 (tttm) cc_final: 0.5176 (ttpt) REVERT: F 198 ASP cc_start: 0.7634 (p0) cc_final: 0.7406 (t70) REVERT: F 202 GLN cc_start: 0.7491 (tp40) cc_final: 0.7117 (mm110) REVERT: G 59 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7193 (mt-10) REVERT: G 130 ARG cc_start: 0.7322 (mtt90) cc_final: 0.6740 (mmm160) REVERT: G 210 MET cc_start: 0.8479 (mtm) cc_final: 0.8088 (mtp) REVERT: G 219 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8422 (tt) REVERT: G 326 MET cc_start: 0.5854 (mmp) cc_final: 0.5242 (mtm) REVERT: H 64 LYS cc_start: 0.5024 (tmmt) cc_final: 0.4271 (mmtt) REVERT: H 100 ILE cc_start: 0.7671 (mm) cc_final: 0.7322 (mm) REVERT: H 118 GLU cc_start: 0.7436 (tt0) cc_final: 0.6866 (pt0) REVERT: H 250 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7172 (ttp-110) outliers start: 75 outliers final: 49 residues processed: 365 average time/residue: 0.3293 time to fit residues: 177.4713 Evaluate side-chains 352 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN C 330 ASN D 200 GLN F 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18343 Z= 0.208 Angle : 0.664 8.391 24746 Z= 0.315 Chirality : 0.042 0.162 2840 Planarity : 0.004 0.061 3163 Dihedral : 7.924 116.707 2629 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.76 % Favored : 92.71 % Rotamer: Outliers : 3.78 % Allowed : 19.53 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2277 helix: 0.09 (0.16), residues: 1087 sheet: -2.04 (0.30), residues: 278 loop : -2.24 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 294 PHE 0.025 0.001 PHE A 327 TYR 0.015 0.001 TYR E 315 ARG 0.006 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7800 (p) cc_final: 0.7525 (t) REVERT: B 178 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7183 (m-10) REVERT: B 229 ARG cc_start: 0.7830 (ttm-80) cc_final: 0.7304 (mtt180) REVERT: B 313 LYS cc_start: 0.6485 (mttp) cc_final: 0.5944 (pttp) REVERT: C 94 GLN cc_start: 0.7014 (pp30) cc_final: 0.6544 (mt0) REVERT: C 101 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7167 (tp40) REVERT: C 202 GLN cc_start: 0.7422 (mp10) cc_final: 0.7083 (tt0) REVERT: C 242 GLN cc_start: 0.7953 (mm110) cc_final: 0.7363 (mm-40) REVERT: C 250 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7223 (mtp-110) REVERT: C 267 ASN cc_start: 0.8130 (t0) cc_final: 0.7925 (t0) REVERT: C 315 TYR cc_start: 0.7303 (t80) cc_final: 0.6653 (t80) REVERT: D 170 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7141 (tpp80) REVERT: D 249 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7502 (mm) REVERT: D 250 ARG cc_start: 0.7532 (tpt170) cc_final: 0.7301 (ttt-90) REVERT: D 332 ASP cc_start: 0.8266 (p0) cc_final: 0.7982 (p0) REVERT: E 94 GLN cc_start: 0.6743 (mt0) cc_final: 0.6404 (mp10) REVERT: E 143 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7436 (p) REVERT: F 43 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: F 64 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7640 (mtpp) REVERT: G 59 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7162 (mt-10) REVERT: G 130 ARG cc_start: 0.7324 (mtt90) cc_final: 0.6840 (mmt180) REVERT: G 210 MET cc_start: 0.8423 (mtm) cc_final: 0.8017 (mtp) REVERT: G 219 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8334 (tt) REVERT: G 326 MET cc_start: 0.5731 (mmp) cc_final: 0.5371 (mtm) REVERT: H 100 ILE cc_start: 0.7533 (mm) cc_final: 0.7207 (mm) REVERT: H 118 GLU cc_start: 0.7397 (tt0) cc_final: 0.6741 (pt0) REVERT: H 250 ARG cc_start: 0.7433 (ttp-110) cc_final: 0.7172 (ttp-110) outliers start: 70 outliers final: 45 residues processed: 348 average time/residue: 0.3362 time to fit residues: 174.2038 Evaluate side-chains 341 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 151 optimal weight: 0.0040 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 330 ASN C 135 GLN C 330 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18343 Z= 0.242 Angle : 0.681 8.878 24746 Z= 0.324 Chirality : 0.042 0.160 2840 Planarity : 0.004 0.058 3163 Dihedral : 7.636 110.974 2629 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.29 % Favored : 92.18 % Rotamer: Outliers : 3.51 % Allowed : 20.55 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2277 helix: 0.12 (0.16), residues: 1087 sheet: -1.98 (0.30), residues: 278 loop : -2.27 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 294 PHE 0.015 0.001 PHE G 126 TYR 0.016 0.001 TYR E 315 ARG 0.006 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7747 (p) cc_final: 0.7486 (t) REVERT: B 154 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7116 (tm-30) REVERT: B 178 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: B 229 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7439 (mtt180) REVERT: C 84 MET cc_start: 0.7542 (mtm) cc_final: 0.7263 (mtm) REVERT: C 94 GLN cc_start: 0.7000 (pp30) cc_final: 0.6536 (mt0) REVERT: C 101 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7160 (tp40) REVERT: C 202 GLN cc_start: 0.7440 (mp10) cc_final: 0.7092 (tt0) REVERT: C 242 GLN cc_start: 0.7922 (mm110) cc_final: 0.7335 (mm-40) REVERT: C 250 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7221 (mtp-110) REVERT: C 267 ASN cc_start: 0.8093 (t0) cc_final: 0.7866 (t0) REVERT: C 315 TYR cc_start: 0.7269 (t80) cc_final: 0.6665 (t80) REVERT: D 170 ARG cc_start: 0.7888 (tpp-160) cc_final: 0.7143 (tpp80) REVERT: D 249 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7505 (mm) REVERT: D 250 ARG cc_start: 0.7532 (tpt170) cc_final: 0.7300 (ttt-90) REVERT: D 332 ASP cc_start: 0.8265 (p0) cc_final: 0.8044 (p0) REVERT: E 94 GLN cc_start: 0.6721 (mt0) cc_final: 0.6384 (mp10) REVERT: E 143 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7390 (p) REVERT: E 211 MET cc_start: 0.7812 (mmt) cc_final: 0.7413 (mmt) REVERT: F 29 GLU cc_start: 0.6337 (pp20) cc_final: 0.6124 (pp20) REVERT: F 43 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: F 64 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7645 (mtpp) REVERT: G 130 ARG cc_start: 0.7427 (mtt90) cc_final: 0.6851 (mmm160) REVERT: G 210 MET cc_start: 0.8429 (mtm) cc_final: 0.8022 (mtp) REVERT: G 219 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8352 (tt) REVERT: G 326 MET cc_start: 0.5841 (mmp) cc_final: 0.5398 (mtm) REVERT: H 100 ILE cc_start: 0.7593 (mm) cc_final: 0.7252 (mm) REVERT: H 118 GLU cc_start: 0.7410 (tt0) cc_final: 0.6790 (pt0) REVERT: H 250 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7160 (ttp-110) outliers start: 65 outliers final: 49 residues processed: 339 average time/residue: 0.3250 time to fit residues: 163.0193 Evaluate side-chains 346 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 0.9990 chunk 212 optimal weight: 0.3980 chunk 193 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 89 optimal weight: 0.0270 chunk 162 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN D 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18343 Z= 0.213 Angle : 0.672 10.249 24746 Z= 0.317 Chirality : 0.042 0.160 2840 Planarity : 0.004 0.058 3163 Dihedral : 7.304 100.964 2629 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.90 % Favored : 92.58 % Rotamer: Outliers : 3.29 % Allowed : 21.04 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2277 helix: 0.23 (0.16), residues: 1081 sheet: -1.89 (0.30), residues: 279 loop : -2.21 (0.18), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 294 PHE 0.014 0.001 PHE G 126 TYR 0.021 0.001 TYR B 301 ARG 0.007 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 297 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7737 (p) cc_final: 0.7486 (t) REVERT: B 128 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6254 (pt0) REVERT: B 154 GLU cc_start: 0.7293 (tm-30) cc_final: 0.7033 (tm-30) REVERT: B 178 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: B 229 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7462 (mtt180) REVERT: C 84 MET cc_start: 0.7625 (mtm) cc_final: 0.7337 (mtm) REVERT: C 94 GLN cc_start: 0.6978 (pp30) cc_final: 0.6534 (mt0) REVERT: C 101 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7129 (tp40) REVERT: C 202 GLN cc_start: 0.7398 (mp10) cc_final: 0.7067 (tt0) REVERT: C 242 GLN cc_start: 0.7907 (mm110) cc_final: 0.7325 (mm-40) REVERT: C 250 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7215 (mtp-110) REVERT: C 267 ASN cc_start: 0.8154 (t0) cc_final: 0.7915 (t0) REVERT: C 315 TYR cc_start: 0.7199 (t80) cc_final: 0.6604 (t80) REVERT: D 170 ARG cc_start: 0.7846 (tpp-160) cc_final: 0.7387 (mmm-85) REVERT: D 249 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7502 (mm) REVERT: D 250 ARG cc_start: 0.7523 (tpt170) cc_final: 0.7294 (ttt-90) REVERT: E 94 GLN cc_start: 0.6715 (mt0) cc_final: 0.6357 (mp10) REVERT: E 136 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7066 (mm) REVERT: E 143 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7441 (p) REVERT: E 211 MET cc_start: 0.7762 (mmt) cc_final: 0.7401 (mmt) REVERT: F 43 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: F 64 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7675 (mtpp) REVERT: F 301 TYR cc_start: 0.7734 (t80) cc_final: 0.7495 (t80) REVERT: G 118 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7223 (mt-10) REVERT: G 130 ARG cc_start: 0.7421 (mtt90) cc_final: 0.6867 (mmm160) REVERT: G 210 MET cc_start: 0.8407 (mtm) cc_final: 0.7990 (mtp) REVERT: G 219 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8311 (tt) REVERT: G 326 MET cc_start: 0.5768 (mmp) cc_final: 0.5406 (mtm) REVERT: H 100 ILE cc_start: 0.7524 (mm) cc_final: 0.7182 (mm) REVERT: H 118 GLU cc_start: 0.7410 (tt0) cc_final: 0.6760 (pt0) REVERT: H 250 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.7166 (ttp-110) REVERT: H 304 LYS cc_start: 0.8028 (tttp) cc_final: 0.7535 (tppt) outliers start: 61 outliers final: 49 residues processed: 333 average time/residue: 0.3464 time to fit residues: 170.8142 Evaluate side-chains 346 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 CYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 169 GLU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 151 optimal weight: 0.0270 chunk 229 optimal weight: 0.7980 chunk 210 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN D 200 GLN E 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18343 Z= 0.216 Angle : 0.673 10.419 24746 Z= 0.317 Chirality : 0.042 0.161 2840 Planarity : 0.004 0.056 3163 Dihedral : 7.058 92.550 2629 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.03 % Favored : 92.40 % Rotamer: Outliers : 3.24 % Allowed : 21.47 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2277 helix: 0.26 (0.16), residues: 1080 sheet: -1.85 (0.30), residues: 279 loop : -2.20 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 294 PHE 0.018 0.001 PHE E 126 TYR 0.016 0.001 TYR G 301 ARG 0.010 0.000 ARG E 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 295 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.7731 (p) cc_final: 0.7479 (t) REVERT: A 243 MET cc_start: 0.7063 (ttt) cc_final: 0.6848 (ttp) REVERT: B 128 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6208 (pt0) REVERT: B 154 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7049 (tm-30) REVERT: B 178 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: B 229 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7441 (mtt180) REVERT: C 84 MET cc_start: 0.7624 (mtm) cc_final: 0.7334 (mtm) REVERT: C 94 GLN cc_start: 0.6980 (pp30) cc_final: 0.6533 (mt0) REVERT: C 101 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7123 (tp40) REVERT: C 202 GLN cc_start: 0.7398 (mp10) cc_final: 0.7069 (tt0) REVERT: C 242 GLN cc_start: 0.7902 (mm110) cc_final: 0.7319 (mm-40) REVERT: C 250 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.7217 (mtp-110) REVERT: C 267 ASN cc_start: 0.8202 (t0) cc_final: 0.7951 (t0) REVERT: C 315 TYR cc_start: 0.7203 (t80) cc_final: 0.6610 (t80) REVERT: D 57 LYS cc_start: 0.7999 (mmmm) cc_final: 0.7756 (tppp) REVERT: D 170 ARG cc_start: 0.7839 (tpp-160) cc_final: 0.7393 (mmm-85) REVERT: D 249 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7501 (mm) REVERT: D 250 ARG cc_start: 0.7513 (tpt170) cc_final: 0.7290 (ttt-90) REVERT: E 94 GLN cc_start: 0.6735 (mt0) cc_final: 0.6385 (mp10) REVERT: E 136 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7129 (mm) REVERT: E 143 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7441 (p) REVERT: E 211 MET cc_start: 0.7758 (mmt) cc_final: 0.7359 (mmt) REVERT: E 254 ARG cc_start: 0.7676 (ttt-90) cc_final: 0.7345 (ptm-80) REVERT: F 43 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: F 64 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7629 (mtpp) REVERT: G 118 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7246 (mt-10) REVERT: G 130 ARG cc_start: 0.7443 (mtt90) cc_final: 0.6879 (mmm160) REVERT: G 205 TYR cc_start: 0.7892 (m-10) cc_final: 0.7387 (m-10) REVERT: G 219 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8315 (tt) REVERT: G 326 MET cc_start: 0.5738 (mmp) cc_final: 0.5392 (mtm) REVERT: H 100 ILE cc_start: 0.7543 (mm) cc_final: 0.7201 (mm) REVERT: H 118 GLU cc_start: 0.7415 (tt0) cc_final: 0.6764 (pt0) REVERT: H 250 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.7169 (ttp-110) outliers start: 60 outliers final: 47 residues processed: 331 average time/residue: 0.3337 time to fit residues: 163.5549 Evaluate side-chains 345 residues out of total 1855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain H residue 23 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN C 135 GLN D 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.187227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133939 restraints weight = 18793.100| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.89 r_work: 0.3414 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18343 Z= 0.228 Angle : 0.676 10.874 24746 Z= 0.320 Chirality : 0.042 0.162 2840 Planarity : 0.004 0.055 3163 Dihedral : 6.860 83.361 2629 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.07 % Favored : 92.36 % Rotamer: Outliers : 3.51 % Allowed : 21.20 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2277 helix: 0.27 (0.16), residues: 1080 sheet: -1.90 (0.30), residues: 279 loop : -2.18 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 294 PHE 0.012 0.001 PHE G 327 TYR 0.019 0.001 TYR E 301 ARG 0.010 0.000 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4529.27 seconds wall clock time: 83 minutes 56.07 seconds (5036.07 seconds total)