Starting phenix.real_space_refine on Thu Feb 15 08:51:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef5_28066/02_2024/8ef5_28066_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef5_28066/02_2024/8ef5_28066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef5_28066/02_2024/8ef5_28066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef5_28066/02_2024/8ef5_28066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef5_28066/02_2024/8ef5_28066_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ef5_28066/02_2024/8ef5_28066_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 7619 2.51 5 N 1899 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 213": "NH1" <-> "NH2" Residue "R ARG 260": "NH1" <-> "NH2" Residue "R ARG 275": "NH1" <-> "NH2" Residue "R ARG 282": "NH1" <-> "NH2" Residue "R ARG 347": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 265": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M ARG 347": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11705 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276} Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 436 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "M" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2315 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain: "R" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 165 Unusual residues: {'7V7': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 165 Unusual residues: {'7V7': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.60, per 1000 atoms: 0.56 Number of scatterers: 11705 At special positions: 0 Unit cell: (107.1, 130.662, 141.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2088 8.00 N 1899 7.00 C 7619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 219 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 2.5 seconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 15 sheets defined 45.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'R' and resid 67 through 97 Processing helix chain 'R' and resid 104 through 121 removed outlier: 3.634A pdb=" N TYR R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 132 removed outlier: 3.512A pdb=" N ASN R 129 " --> pdb=" O PHE R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 172 Processing helix chain 'R' and resid 174 through 180 removed outlier: 3.518A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 207 removed outlier: 4.390A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix removed outlier: 3.525A pdb=" N PHE R 206 " --> pdb=" O LEU R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 242 removed outlier: 3.596A pdb=" N ASN R 232 " --> pdb=" O TRP R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 263 removed outlier: 3.504A pdb=" N LEU R 259 " --> pdb=" O GLY R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 307 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 314 through 337 removed outlier: 3.851A pdb=" N HIS R 321 " --> pdb=" O THR R 317 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER R 331 " --> pdb=" O GLY R 327 " (cutoff:3.500A) Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 343 through 351 removed outlier: 3.582A pdb=" N CYS R 348 " --> pdb=" O ASN R 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.545A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.966A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 removed outlier: 4.129A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.566A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.507A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.716A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.604A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 10 through 23 removed outlier: 3.512A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'M' and resid 67 through 97 removed outlier: 3.539A pdb=" N VAL M 96 " --> pdb=" O MET M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 132 removed outlier: 3.576A pdb=" N TYR M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU M 123 " --> pdb=" O ALA M 119 " (cutoff:3.500A) Proline residue: M 124 - end of helix removed outlier: 3.523A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 172 removed outlier: 3.799A pdb=" N PHE M 154 " --> pdb=" O TYR M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 4.237A pdb=" N ASP M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 207 removed outlier: 3.543A pdb=" N ILE M 188 " --> pdb=" O ARG M 184 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP M 194 " --> pdb=" O ASN M 190 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Proline residue: M 203 - end of helix removed outlier: 3.634A pdb=" N PHE M 206 " --> pdb=" O LEU M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 242 Processing helix chain 'M' and resid 244 through 263 removed outlier: 3.574A pdb=" N LEU M 259 " --> pdb=" O GLY M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 307 removed outlier: 3.662A pdb=" N ASN M 276 " --> pdb=" O GLU M 272 " (cutoff:3.500A) Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 314 through 338 removed outlier: 3.552A pdb=" N ASN M 330 " --> pdb=" O LEU M 326 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 335 - end of helix Processing helix chain 'M' and resid 343 through 351 Processing helix chain 'F' and resid 338 through 351 Processing sheet with id= A, first strand: chain 'R' and resid 208 through 213 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.762A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.809A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.792A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.721A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.346A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.737A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.875A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.608A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.740A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER E 120 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 147 through 149 removed outlier: 7.025A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 156 through 161 Processing sheet with id= N, first strand: chain 'E' and resid 227 through 232 removed outlier: 6.075A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 208 through 213 removed outlier: 3.522A pdb=" N THR M 220 " --> pdb=" O THR M 209 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1734 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: 3.84 Time building geometry restraints manager: 5.02 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: 3020 1.34 - 1.46: 2424 1.46 - 1.58: 6394 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 11984 Sorted by residual: bond pdb=" C02 7V7 M 501 " pdb=" N05 7V7 M 501 " ideal model delta sigma weight residual 1.359 1.436 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C02 7V7 R 501 " pdb=" N05 7V7 R 501 " ideal model delta sigma weight residual 1.359 1.435 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C20 7V7 M 501 " pdb=" N05 7V7 M 501 " ideal model delta sigma weight residual 1.423 1.493 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C20 7V7 R 501 " pdb=" N05 7V7 R 501 " ideal model delta sigma weight residual 1.423 1.492 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 CLR R 505 " pdb=" C6 CLR R 505 " ideal model delta sigma weight residual 1.332 1.298 0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 11979 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.41: 236 105.41 - 112.59: 6391 112.59 - 119.77: 3813 119.77 - 126.96: 5732 126.96 - 134.14: 133 Bond angle restraints: 16305 Sorted by residual: angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 121.54 133.67 -12.13 1.91e+00 2.74e-01 4.03e+01 angle pdb=" C GLY E 210 " pdb=" N THR E 211 " pdb=" CA THR E 211 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 angle pdb=" N ASP E 74 " pdb=" CA ASP E 74 " pdb=" C ASP E 74 " ideal model delta sigma weight residual 109.81 116.71 -6.90 2.21e+00 2.05e-01 9.76e+00 angle pdb=" N LEU M 123 " pdb=" CA LEU M 123 " pdb=" C LEU M 123 " ideal model delta sigma weight residual 109.81 116.39 -6.58 2.21e+00 2.05e-01 8.86e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 124.31 129.22 -4.91 1.67e+00 3.59e-01 8.64e+00 ... (remaining 16300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 7330 16.39 - 32.78: 226 32.78 - 49.18: 20 49.18 - 65.57: 3 65.57 - 81.96: 2 Dihedral angle restraints: 7581 sinusoidal: 3368 harmonic: 4213 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CB CYS M 142 " pdb=" SG CYS M 142 " pdb=" SG CYS M 219 " pdb=" CB CYS M 219 " ideal model delta sinusoidal sigma weight residual 93.00 123.38 -30.38 1 1.00e+01 1.00e-02 1.32e+01 ... (remaining 7578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1694 0.085 - 0.169: 164 0.169 - 0.254: 26 0.254 - 0.339: 11 0.339 - 0.424: 10 Chirality restraints: 1905 Sorted by residual: chirality pdb=" C14 CLR M 502 " pdb=" C13 CLR M 502 " pdb=" C15 CLR M 502 " pdb=" C8 CLR M 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C14 CLR M 504 " pdb=" C13 CLR M 504 " pdb=" C15 CLR M 504 " pdb=" C8 CLR M 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 1902 not shown) Planarity restraints: 1964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 7V7 R 501 " 0.031 2.00e-02 2.50e+03 3.11e-01 1.45e+03 pdb=" C03 7V7 R 501 " -0.394 2.00e-02 2.50e+03 pdb=" C06 7V7 R 501 " -0.374 2.00e-02 2.50e+03 pdb=" C20 7V7 R 501 " 0.330 2.00e-02 2.50e+03 pdb=" N05 7V7 R 501 " -0.010 2.00e-02 2.50e+03 pdb=" O01 7V7 R 501 " 0.417 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 7V7 M 501 " -0.032 2.00e-02 2.50e+03 3.09e-01 1.44e+03 pdb=" C03 7V7 M 501 " 0.392 2.00e-02 2.50e+03 pdb=" C06 7V7 M 501 " 0.374 2.00e-02 2.50e+03 pdb=" C20 7V7 M 501 " -0.327 2.00e-02 2.50e+03 pdb=" N05 7V7 M 501 " 0.009 2.00e-02 2.50e+03 pdb=" O01 7V7 M 501 " -0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO B 236 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.046 5.00e-02 4.00e+02 ... (remaining 1961 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2751 2.81 - 3.33: 10547 3.33 - 3.85: 18711 3.85 - 4.38: 21361 4.38 - 4.90: 37904 Nonbonded interactions: 91274 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.284 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.291 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.309 2.440 nonbonded pdb=" O ILE E 139 " pdb=" OG1 THR E 239 " model vdw 2.319 2.440 nonbonded pdb=" O ALA M 325 " pdb=" OG1 THR M 329 " model vdw 2.324 2.440 ... (remaining 91269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'M' and (resid 66 through 352 or resid 501 through 506)) selection = chain 'R' } 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: 0.590 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: 0.010 Extract box with map and model: 2.860 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.000 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11984 Z= 0.292 Angle : 0.882 12.130 16305 Z= 0.474 Chirality : 0.066 0.424 1905 Planarity : 0.012 0.311 1964 Dihedral : 8.234 81.961 4848 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1423 helix: 0.88 (0.18), residues: 638 sheet: 0.35 (0.30), residues: 274 loop : -1.23 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 135 HIS 0.006 0.001 HIS B 225 PHE 0.020 0.002 PHE B 234 TYR 0.023 0.002 TYR M 151 ARG 0.007 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 PHE cc_start: 0.7583 (m-80) cc_final: 0.7367 (m-80) REVERT: R 145 VAL cc_start: 0.7276 (t) cc_final: 0.6913 (t) REVERT: R 185 ASN cc_start: 0.8093 (t0) cc_final: 0.7866 (t0) REVERT: R 282 ARG cc_start: 0.8319 (ttp-170) cc_final: 0.8103 (ttp-170) REVERT: R 303 ILE cc_start: 0.8080 (mm) cc_final: 0.7639 (mt) REVERT: A 8 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7226 (mt-10) REVERT: A 10 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7602 (mtmt) REVERT: A 14 GLU cc_start: 0.7450 (tt0) cc_final: 0.7173 (tt0) REVERT: A 17 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7929 (mmmt) REVERT: A 29 LYS cc_start: 0.8317 (tttt) cc_final: 0.8050 (tttt) REVERT: A 49 ILE cc_start: 0.8118 (tt) cc_final: 0.7448 (mm) REVERT: A 193 ASP cc_start: 0.7383 (t0) cc_final: 0.7174 (t0) REVERT: A 197 LYS cc_start: 0.8113 (mttt) cc_final: 0.7883 (mttt) REVERT: A 231 ASP cc_start: 0.7032 (t0) cc_final: 0.6615 (t0) REVERT: A 247 MET cc_start: 0.7933 (mtt) cc_final: 0.7522 (mtm) REVERT: A 251 ASP cc_start: 0.7409 (t0) cc_final: 0.7183 (t0) REVERT: A 272 ASP cc_start: 0.8085 (p0) cc_final: 0.7794 (p0) REVERT: A 273 LEU cc_start: 0.8792 (mt) cc_final: 0.8453 (tt) REVERT: A 274 PHE cc_start: 0.8509 (t80) cc_final: 0.7938 (t80) REVERT: A 304 GLN cc_start: 0.7986 (tt0) cc_final: 0.7637 (tt0) REVERT: A 308 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 316 THR cc_start: 0.8027 (m) cc_final: 0.7731 (p) REVERT: B 17 GLN cc_start: 0.8256 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 38 ASP cc_start: 0.8507 (p0) cc_final: 0.7848 (p0) REVERT: B 50 THR cc_start: 0.8217 (m) cc_final: 0.7604 (t) REVERT: B 52 ARG cc_start: 0.7677 (mtt90) cc_final: 0.7453 (mtt90) REVERT: B 87 THR cc_start: 0.8521 (m) cc_final: 0.8221 (t) REVERT: B 171 ILE cc_start: 0.8617 (mt) cc_final: 0.8375 (mm) REVERT: B 188 MET cc_start: 0.7204 (mmm) cc_final: 0.6872 (mmt) REVERT: B 221 THR cc_start: 0.8391 (m) cc_final: 0.7998 (p) REVERT: B 258 ASP cc_start: 0.7980 (t0) cc_final: 0.7664 (t70) REVERT: E 231 MET cc_start: 0.7554 (ttp) cc_final: 0.7347 (ttm) REVERT: E 232 GLN cc_start: 0.7867 (pp30) cc_final: 0.7531 (pp30) REVERT: M 145 VAL cc_start: 0.7598 (t) cc_final: 0.7307 (p) REVERT: M 283 MET cc_start: 0.8220 (tpp) cc_final: 0.7966 (tpp) REVERT: F 341 ASP cc_start: 0.7697 (t0) cc_final: 0.7353 (t0) REVERT: F 345 LYS cc_start: 0.8415 (tttt) cc_final: 0.8134 (tttp) REVERT: F 349 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7719 (mtmm) outliers start: 0 outliers final: 0 residues processed: 508 average time/residue: 0.2732 time to fit residues: 187.4300 Evaluate side-chains 408 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0670 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 190 ASN A 188 HIS A 204 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 266 HIS E 180 GLN E 232 GLN E 233 HIS M 106 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11984 Z= 0.168 Angle : 0.557 10.960 16305 Z= 0.287 Chirality : 0.041 0.221 1905 Planarity : 0.004 0.057 1964 Dihedral : 5.889 88.111 2245 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.10 % Allowed : 12.94 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1423 helix: 2.06 (0.18), residues: 648 sheet: 0.43 (0.30), residues: 277 loop : -1.14 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 320 HIS 0.004 0.001 HIS C 44 PHE 0.026 0.001 PHE B 241 TYR 0.019 0.002 TYR B 59 ARG 0.009 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 406 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 72 THR cc_start: 0.8288 (t) cc_final: 0.8007 (p) REVERT: R 207 MET cc_start: 0.7578 (mtm) cc_final: 0.7335 (mtm) REVERT: R 209 THR cc_start: 0.8324 (p) cc_final: 0.8030 (p) REVERT: R 222 THR cc_start: 0.7786 (m) cc_final: 0.7563 (p) REVERT: R 266 MET cc_start: 0.6758 (tmm) cc_final: 0.6440 (tmm) REVERT: R 278 ARG cc_start: 0.7264 (ttm170) cc_final: 0.7054 (ttm170) REVERT: R 282 ARG cc_start: 0.8256 (ttp-170) cc_final: 0.8049 (ttp-170) REVERT: A 14 GLU cc_start: 0.7255 (tt0) cc_final: 0.6952 (tt0) REVERT: A 17 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7861 (mmmt) REVERT: A 21 ARG cc_start: 0.7289 (ttp80) cc_final: 0.7007 (ttp80) REVERT: A 29 LYS cc_start: 0.8606 (tttt) cc_final: 0.8272 (tttt) REVERT: A 33 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6886 (mt-10) REVERT: A 197 LYS cc_start: 0.8414 (mttt) cc_final: 0.8005 (mttt) REVERT: A 231 ASP cc_start: 0.7116 (t0) cc_final: 0.6868 (t0) REVERT: A 247 MET cc_start: 0.7969 (mtt) cc_final: 0.7587 (mtm) REVERT: A 274 PHE cc_start: 0.8501 (t80) cc_final: 0.7990 (t80) REVERT: A 275 GLU cc_start: 0.7326 (pt0) cc_final: 0.7010 (pt0) REVERT: A 276 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7375 (mp0) REVERT: A 308 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 310 LEU cc_start: 0.9173 (mt) cc_final: 0.8819 (mt) REVERT: A 312 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7774 (mptp) REVERT: A 316 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7742 (p) REVERT: A 317 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8356 (tttt) REVERT: B 17 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 38 ASP cc_start: 0.8505 (p0) cc_final: 0.7835 (p0) REVERT: B 50 THR cc_start: 0.8259 (m) cc_final: 0.7663 (t) REVERT: B 89 LYS cc_start: 0.8786 (mttp) cc_final: 0.8522 (mttp) REVERT: B 111 TYR cc_start: 0.8694 (m-80) cc_final: 0.8468 (m-80) REVERT: B 170 ASP cc_start: 0.7316 (t0) cc_final: 0.6809 (t0) REVERT: B 188 MET cc_start: 0.7625 (mmm) cc_final: 0.7383 (mmt) REVERT: B 221 THR cc_start: 0.8488 (m) cc_final: 0.8058 (p) REVERT: B 229 ILE cc_start: 0.8405 (mt) cc_final: 0.8042 (mp) REVERT: B 234 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.6705 (t80) REVERT: B 289 TYR cc_start: 0.7661 (m-80) cc_final: 0.7363 (m-80) REVERT: C 13 ARG cc_start: 0.8699 (ttp-110) cc_final: 0.8470 (mtm110) REVERT: E 231 MET cc_start: 0.7615 (ttp) cc_final: 0.7271 (ttm) REVERT: M 150 TYR cc_start: 0.8415 (m-80) cc_final: 0.8123 (m-80) REVERT: M 176 LYS cc_start: 0.8653 (mttp) cc_final: 0.8450 (mttp) REVERT: M 190 ASN cc_start: 0.7413 (m-40) cc_final: 0.7141 (m-40) REVERT: M 245 MET cc_start: 0.7218 (tpp) cc_final: 0.6910 (mpp) REVERT: M 283 MET cc_start: 0.8043 (tpp) cc_final: 0.7831 (tpp) REVERT: F 345 LYS cc_start: 0.8482 (tttt) cc_final: 0.8245 (tttp) REVERT: F 349 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7758 (mtmm) outliers start: 39 outliers final: 21 residues processed: 422 average time/residue: 0.2757 time to fit residues: 157.4891 Evaluate side-chains 414 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 391 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS R 321 HIS A 22 ASN A 331 ASN B 110 ASN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11984 Z= 0.204 Angle : 0.541 10.161 16305 Z= 0.277 Chirality : 0.040 0.200 1905 Planarity : 0.004 0.048 1964 Dihedral : 5.790 77.960 2245 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 4.29 % Allowed : 15.16 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.22 (0.21), residues: 1423 helix: 2.33 (0.19), residues: 651 sheet: 0.33 (0.31), residues: 280 loop : -1.01 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.021 0.001 PHE A 334 TYR 0.022 0.002 TYR R 130 ARG 0.005 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 400 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8332 (mt) cc_final: 0.8049 (mt) REVERT: R 221 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8500 (mp) REVERT: A 14 GLU cc_start: 0.7265 (tt0) cc_final: 0.6956 (tt0) REVERT: A 17 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7896 (mmmt) REVERT: A 18 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6697 (tmm) REVERT: A 21 ARG cc_start: 0.7277 (ttp80) cc_final: 0.7068 (ttp80) REVERT: A 29 LYS cc_start: 0.8600 (tttt) cc_final: 0.8325 (tttt) REVERT: A 231 ASP cc_start: 0.7324 (t0) cc_final: 0.7044 (t0) REVERT: A 242 ARG cc_start: 0.7537 (ttm170) cc_final: 0.7281 (ttm170) REVERT: A 247 MET cc_start: 0.8098 (mtt) cc_final: 0.7664 (mtm) REVERT: A 272 ASP cc_start: 0.7968 (p0) cc_final: 0.7381 (p0) REVERT: A 275 GLU cc_start: 0.7373 (pt0) cc_final: 0.7096 (pp20) REVERT: A 308 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 316 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7807 (p) REVERT: B 17 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 74 SER cc_start: 0.8544 (t) cc_final: 0.8001 (p) REVERT: B 96 ARG cc_start: 0.6973 (mtt90) cc_final: 0.6590 (mtt90) REVERT: B 111 TYR cc_start: 0.8707 (m-80) cc_final: 0.8482 (m-80) REVERT: B 138 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6572 (mt-10) REVERT: B 163 ASP cc_start: 0.7756 (p0) cc_final: 0.7414 (p0) REVERT: B 188 MET cc_start: 0.7841 (mmm) cc_final: 0.6805 (mmm) REVERT: B 198 LEU cc_start: 0.9108 (mt) cc_final: 0.8883 (mp) REVERT: B 212 ASP cc_start: 0.7432 (p0) cc_final: 0.6871 (p0) REVERT: B 221 THR cc_start: 0.8474 (m) cc_final: 0.8131 (p) REVERT: B 229 ILE cc_start: 0.8510 (mt) cc_final: 0.8154 (mp) REVERT: B 234 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6792 (t80) REVERT: B 261 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8374 (tt) REVERT: B 289 TYR cc_start: 0.7817 (m-80) cc_final: 0.7501 (m-80) REVERT: E 115 THR cc_start: 0.7957 (t) cc_final: 0.7641 (p) REVERT: E 191 TYR cc_start: 0.8599 (p90) cc_final: 0.8380 (p90) REVERT: E 231 MET cc_start: 0.7922 (ttp) cc_final: 0.7711 (ttt) REVERT: E 232 GLN cc_start: 0.8199 (pp30) cc_final: 0.7723 (pp30) REVERT: M 148 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7311 (mm) REVERT: M 150 TYR cc_start: 0.8407 (m-80) cc_final: 0.8155 (m-80) REVERT: M 222 THR cc_start: 0.8619 (t) cc_final: 0.8274 (p) REVERT: M 236 ILE cc_start: 0.8565 (mm) cc_final: 0.8325 (mt) REVERT: M 245 MET cc_start: 0.7424 (tpp) cc_final: 0.6926 (mpp) REVERT: M 283 MET cc_start: 0.8013 (tpp) cc_final: 0.7765 (tpp) REVERT: F 345 LYS cc_start: 0.8473 (tttt) cc_final: 0.8260 (tttp) REVERT: F 349 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7698 (mtmm) outliers start: 54 outliers final: 33 residues processed: 420 average time/residue: 0.2741 time to fit residues: 156.1970 Evaluate side-chains 414 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 375 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN M 152 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11984 Z= 0.193 Angle : 0.529 10.273 16305 Z= 0.270 Chirality : 0.040 0.181 1905 Planarity : 0.004 0.044 1964 Dihedral : 5.705 69.018 2245 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.68 % Allowed : 18.10 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.27 (0.21), residues: 1423 helix: 2.32 (0.19), residues: 648 sheet: 0.32 (0.31), residues: 280 loop : -0.84 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 111 HIS 0.004 0.001 HIS E 35 PHE 0.024 0.001 PHE A 334 TYR 0.021 0.002 TYR M 93 ARG 0.007 0.001 ARG M 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 381 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8297 (mt) cc_final: 0.8040 (mt) REVERT: R 221 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8565 (mp) REVERT: A 14 GLU cc_start: 0.7312 (tt0) cc_final: 0.6996 (tt0) REVERT: A 17 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7911 (mmmt) REVERT: A 18 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6663 (tmm) REVERT: A 21 ARG cc_start: 0.7295 (ttp80) cc_final: 0.7076 (ttp80) REVERT: A 25 GLU cc_start: 0.7661 (tt0) cc_final: 0.7389 (tt0) REVERT: A 29 LYS cc_start: 0.8566 (tttt) cc_final: 0.8356 (tttt) REVERT: A 33 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 197 LYS cc_start: 0.8306 (mttt) cc_final: 0.8014 (mttt) REVERT: A 231 ASP cc_start: 0.7303 (t0) cc_final: 0.7021 (t0) REVERT: A 247 MET cc_start: 0.8136 (mtt) cc_final: 0.7733 (mtm) REVERT: A 272 ASP cc_start: 0.7894 (p0) cc_final: 0.7339 (p0) REVERT: A 275 GLU cc_start: 0.7329 (pt0) cc_final: 0.7057 (pp20) REVERT: A 316 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7810 (p) REVERT: A 317 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8397 (tttt) REVERT: A 330 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7951 (mmtt) REVERT: A 350 ASP cc_start: 0.8516 (t0) cc_final: 0.8257 (t0) REVERT: B 17 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 74 SER cc_start: 0.8520 (t) cc_final: 0.8070 (p) REVERT: B 96 ARG cc_start: 0.7121 (mtt90) cc_final: 0.6754 (mtt90) REVERT: B 111 TYR cc_start: 0.8727 (m-80) cc_final: 0.8487 (m-80) REVERT: B 163 ASP cc_start: 0.7849 (p0) cc_final: 0.7536 (p0) REVERT: B 198 LEU cc_start: 0.9094 (mt) cc_final: 0.8858 (mm) REVERT: B 214 ARG cc_start: 0.7135 (ttp80) cc_final: 0.6899 (ttp80) REVERT: B 221 THR cc_start: 0.8364 (m) cc_final: 0.8049 (p) REVERT: B 254 ASP cc_start: 0.7183 (t0) cc_final: 0.6895 (t0) REVERT: B 277 SER cc_start: 0.8396 (t) cc_final: 0.8160 (t) REVERT: E 115 THR cc_start: 0.7989 (t) cc_final: 0.7649 (p) REVERT: E 202 ASP cc_start: 0.7318 (t70) cc_final: 0.7006 (t70) REVERT: E 231 MET cc_start: 0.8024 (ttp) cc_final: 0.7797 (ttt) REVERT: E 232 GLN cc_start: 0.8403 (pp30) cc_final: 0.7897 (pp30) REVERT: M 150 TYR cc_start: 0.8317 (m-80) cc_final: 0.8006 (m-80) REVERT: M 194 TRP cc_start: 0.8128 (m100) cc_final: 0.7549 (m100) REVERT: M 200 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7913 (tt) REVERT: M 222 THR cc_start: 0.8677 (t) cc_final: 0.8341 (p) REVERT: M 236 ILE cc_start: 0.8552 (mm) cc_final: 0.8300 (mt) REVERT: M 245 MET cc_start: 0.7313 (tpp) cc_final: 0.6972 (mpp) REVERT: M 312 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7646 (tm-30) REVERT: F 345 LYS cc_start: 0.8469 (tttt) cc_final: 0.8253 (tttp) REVERT: F 349 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7693 (mtmm) outliers start: 59 outliers final: 37 residues processed: 405 average time/residue: 0.2746 time to fit residues: 150.2691 Evaluate side-chains 414 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 372 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 132 MET Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 0.0270 chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 110 ASN E 180 GLN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11984 Z= 0.209 Angle : 0.539 10.462 16305 Z= 0.276 Chirality : 0.041 0.249 1905 Planarity : 0.004 0.044 1964 Dihedral : 5.729 69.933 2245 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.60 % Allowed : 18.81 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.28 (0.22), residues: 1423 helix: 2.27 (0.19), residues: 649 sheet: 0.17 (0.30), residues: 292 loop : -0.67 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.001 PHE A 334 TYR 0.022 0.002 TYR M 93 ARG 0.007 0.001 ARG M 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 369 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8244 (mt) cc_final: 0.7974 (mt) REVERT: R 101 MET cc_start: 0.6962 (mtp) cc_final: 0.6720 (mtp) REVERT: R 221 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8675 (mp) REVERT: R 266 MET cc_start: 0.7181 (tmm) cc_final: 0.6648 (tmm) REVERT: A 14 GLU cc_start: 0.7298 (tt0) cc_final: 0.6998 (tt0) REVERT: A 17 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7930 (mmmt) REVERT: A 18 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6674 (tmm) REVERT: A 21 ARG cc_start: 0.7285 (ttp80) cc_final: 0.7085 (ttp80) REVERT: A 25 GLU cc_start: 0.7644 (tt0) cc_final: 0.7369 (tt0) REVERT: A 33 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 197 LYS cc_start: 0.8285 (mttt) cc_final: 0.8018 (mttt) REVERT: A 210 LYS cc_start: 0.8592 (mmmm) cc_final: 0.7598 (tttm) REVERT: A 231 ASP cc_start: 0.7397 (t0) cc_final: 0.7124 (t0) REVERT: A 272 ASP cc_start: 0.7899 (p0) cc_final: 0.7282 (p0) REVERT: A 273 LEU cc_start: 0.8765 (mt) cc_final: 0.8467 (tt) REVERT: A 275 GLU cc_start: 0.7347 (pt0) cc_final: 0.7125 (pp20) REVERT: A 316 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7822 (p) REVERT: A 330 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7918 (mmtt) REVERT: B 17 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 74 SER cc_start: 0.8464 (t) cc_final: 0.8137 (p) REVERT: B 96 ARG cc_start: 0.7193 (mtt90) cc_final: 0.6837 (mtt90) REVERT: B 111 TYR cc_start: 0.8727 (m-80) cc_final: 0.8461 (m-80) REVERT: B 188 MET cc_start: 0.7113 (mmm) cc_final: 0.6506 (mmm) REVERT: B 198 LEU cc_start: 0.9102 (mt) cc_final: 0.8843 (mm) REVERT: B 200 VAL cc_start: 0.8914 (p) cc_final: 0.8633 (m) REVERT: B 214 ARG cc_start: 0.7171 (ttp80) cc_final: 0.6951 (ttp80) REVERT: B 221 THR cc_start: 0.8410 (m) cc_final: 0.8090 (p) REVERT: B 254 ASP cc_start: 0.7156 (t0) cc_final: 0.6881 (t0) REVERT: B 277 SER cc_start: 0.8388 (t) cc_final: 0.8156 (t) REVERT: E 77 ASN cc_start: 0.8625 (t0) cc_final: 0.8369 (t0) REVERT: E 115 THR cc_start: 0.8021 (t) cc_final: 0.7656 (p) REVERT: E 202 ASP cc_start: 0.7402 (t70) cc_final: 0.7064 (t70) REVERT: E 231 MET cc_start: 0.7997 (ttp) cc_final: 0.7772 (ttt) REVERT: E 232 GLN cc_start: 0.8397 (pp30) cc_final: 0.7877 (pp30) REVERT: M 200 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7941 (tt) REVERT: M 222 THR cc_start: 0.8834 (t) cc_final: 0.8540 (p) REVERT: M 245 MET cc_start: 0.7324 (tpp) cc_final: 0.7051 (mpp) REVERT: F 345 LYS cc_start: 0.8471 (tttt) cc_final: 0.8249 (tttp) REVERT: F 349 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7699 (mtmm) outliers start: 58 outliers final: 40 residues processed: 396 average time/residue: 0.2794 time to fit residues: 149.9640 Evaluate side-chains 404 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 359 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 317 THR Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 0.0770 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11984 Z= 0.156 Angle : 0.544 12.835 16305 Z= 0.271 Chirality : 0.040 0.177 1905 Planarity : 0.004 0.043 1964 Dihedral : 5.540 71.406 2245 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.33 % Allowed : 19.92 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.40 (0.22), residues: 1423 helix: 2.37 (0.19), residues: 653 sheet: 0.21 (0.30), residues: 291 loop : -0.62 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.000 HIS E 35 PHE 0.017 0.001 PHE A 334 TYR 0.021 0.001 TYR M 93 ARG 0.007 0.001 ARG R 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 370 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8222 (mt) cc_final: 0.7940 (mt) REVERT: R 101 MET cc_start: 0.6936 (mtp) cc_final: 0.6727 (mtp) REVERT: R 131 LEU cc_start: 0.8531 (tp) cc_final: 0.8281 (tp) REVERT: R 209 THR cc_start: 0.8114 (p) cc_final: 0.7823 (p) REVERT: R 221 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8626 (mp) REVERT: R 266 MET cc_start: 0.7268 (tmm) cc_final: 0.6929 (tmm) REVERT: A 14 GLU cc_start: 0.7250 (tt0) cc_final: 0.6974 (tt0) REVERT: A 17 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7915 (mmmt) REVERT: A 18 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6590 (tmm) REVERT: A 25 GLU cc_start: 0.7623 (tt0) cc_final: 0.7372 (tt0) REVERT: A 33 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6963 (mt-10) REVERT: A 197 LYS cc_start: 0.8313 (mttt) cc_final: 0.7866 (mttt) REVERT: A 210 LYS cc_start: 0.8547 (mmmm) cc_final: 0.7543 (tttm) REVERT: A 231 ASP cc_start: 0.7387 (t0) cc_final: 0.7138 (t0) REVERT: A 242 ARG cc_start: 0.7638 (ttm170) cc_final: 0.7380 (ttm170) REVERT: A 272 ASP cc_start: 0.7831 (p0) cc_final: 0.7569 (p0) REVERT: A 273 LEU cc_start: 0.8733 (mt) cc_final: 0.8463 (tt) REVERT: A 316 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7820 (p) REVERT: B 17 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 74 SER cc_start: 0.8403 (t) cc_final: 0.8110 (p) REVERT: B 96 ARG cc_start: 0.7168 (mtt90) cc_final: 0.6803 (mtt90) REVERT: B 111 TYR cc_start: 0.8710 (m-80) cc_final: 0.8432 (m-80) REVERT: B 188 MET cc_start: 0.7145 (mmm) cc_final: 0.6613 (mmm) REVERT: B 198 LEU cc_start: 0.9071 (mt) cc_final: 0.8810 (mm) REVERT: B 200 VAL cc_start: 0.8917 (p) cc_final: 0.8614 (m) REVERT: B 214 ARG cc_start: 0.7175 (ttp80) cc_final: 0.6926 (ttp80) REVERT: B 221 THR cc_start: 0.8336 (m) cc_final: 0.8046 (p) REVERT: B 254 ASP cc_start: 0.7128 (t0) cc_final: 0.6863 (t0) REVERT: E 115 THR cc_start: 0.8017 (t) cc_final: 0.7612 (p) REVERT: E 231 MET cc_start: 0.8004 (ttp) cc_final: 0.7767 (ttt) REVERT: M 200 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7861 (tt) REVERT: M 245 MET cc_start: 0.7152 (tpp) cc_final: 0.6926 (tpp) REVERT: M 312 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7786 (tm-30) REVERT: F 345 LYS cc_start: 0.8455 (tttt) cc_final: 0.8236 (tttp) REVERT: F 349 LYS cc_start: 0.7925 (mtpt) cc_final: 0.7666 (mtmm) outliers start: 42 outliers final: 29 residues processed: 390 average time/residue: 0.2752 time to fit residues: 145.3224 Evaluate side-chains 388 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 355 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 317 THR Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11984 Z= 0.205 Angle : 0.566 10.725 16305 Z= 0.285 Chirality : 0.040 0.174 1905 Planarity : 0.004 0.043 1964 Dihedral : 5.700 73.592 2245 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.89 % Allowed : 19.60 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.35 (0.22), residues: 1423 helix: 2.29 (0.19), residues: 653 sheet: 0.16 (0.30), residues: 292 loop : -0.56 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.022 0.001 PHE A 334 TYR 0.030 0.002 TYR R 130 ARG 0.008 0.001 ARG R 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 363 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8188 (mt) cc_final: 0.7932 (mt) REVERT: R 101 MET cc_start: 0.6964 (mtp) cc_final: 0.6715 (mtp) REVERT: R 221 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 14 GLU cc_start: 0.7287 (tt0) cc_final: 0.7027 (tt0) REVERT: A 17 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7957 (mmmt) REVERT: A 18 MET cc_start: 0.7312 (tmm) cc_final: 0.6690 (tmm) REVERT: A 33 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7111 (mt-10) REVERT: A 197 LYS cc_start: 0.8311 (mttt) cc_final: 0.7923 (mttt) REVERT: A 231 ASP cc_start: 0.7444 (t0) cc_final: 0.7177 (t0) REVERT: A 242 ARG cc_start: 0.7518 (ttm170) cc_final: 0.7186 (ttm170) REVERT: A 243 MET cc_start: 0.8664 (mmp) cc_final: 0.8351 (tpp) REVERT: A 275 GLU cc_start: 0.6977 (pp20) cc_final: 0.6676 (pp20) REVERT: A 316 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7876 (p) REVERT: B 17 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 111 TYR cc_start: 0.8713 (m-80) cc_final: 0.8466 (m-80) REVERT: B 200 VAL cc_start: 0.8942 (p) cc_final: 0.8667 (m) REVERT: B 214 ARG cc_start: 0.7224 (ttp80) cc_final: 0.6954 (ttp80) REVERT: B 220 GLN cc_start: 0.8064 (mp10) cc_final: 0.7763 (mp10) REVERT: B 221 THR cc_start: 0.8356 (m) cc_final: 0.8042 (p) REVERT: B 254 ASP cc_start: 0.7178 (t0) cc_final: 0.6916 (t0) REVERT: B 277 SER cc_start: 0.8347 (t) cc_final: 0.8105 (t) REVERT: E 77 ASN cc_start: 0.8544 (t0) cc_final: 0.8344 (t0) REVERT: E 115 THR cc_start: 0.8042 (t) cc_final: 0.7648 (p) REVERT: E 202 ASP cc_start: 0.7434 (t70) cc_final: 0.7096 (t70) REVERT: M 200 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7904 (tt) REVERT: M 245 MET cc_start: 0.7174 (tpp) cc_final: 0.6935 (tpp) REVERT: F 345 LYS cc_start: 0.8474 (tttt) cc_final: 0.8248 (tttp) REVERT: F 349 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7672 (mtmm) outliers start: 49 outliers final: 40 residues processed: 386 average time/residue: 0.2881 time to fit residues: 150.0922 Evaluate side-chains 388 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 345 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 317 THR Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 106 optimal weight: 0.4980 chunk 122 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN M 152 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11984 Z= 0.168 Angle : 0.568 10.747 16305 Z= 0.285 Chirality : 0.040 0.197 1905 Planarity : 0.004 0.060 1964 Dihedral : 5.592 73.916 2245 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.73 % Allowed : 20.48 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.41 (0.22), residues: 1423 helix: 2.33 (0.19), residues: 649 sheet: 0.18 (0.29), residues: 307 loop : -0.52 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE R 110 TYR 0.022 0.001 TYR R 130 ARG 0.008 0.001 ARG R 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 353 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 MET cc_start: 0.6993 (mmm) cc_final: 0.6676 (mmm) REVERT: R 79 ILE cc_start: 0.8194 (mt) cc_final: 0.7888 (mt) REVERT: R 101 MET cc_start: 0.7012 (mtp) cc_final: 0.6785 (mtp) REVERT: R 221 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8650 (mp) REVERT: A 14 GLU cc_start: 0.7280 (tt0) cc_final: 0.7047 (tt0) REVERT: A 17 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7842 (mtmm) REVERT: A 18 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6640 (tmm) REVERT: A 29 LYS cc_start: 0.8557 (tttt) cc_final: 0.8242 (ttmm) REVERT: A 33 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7103 (mt-10) REVERT: A 197 LYS cc_start: 0.8311 (mttt) cc_final: 0.7915 (mttt) REVERT: A 231 ASP cc_start: 0.7467 (t0) cc_final: 0.7188 (t0) REVERT: A 242 ARG cc_start: 0.7560 (ttm170) cc_final: 0.7190 (ttm170) REVERT: A 316 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7939 (p) REVERT: B 17 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 111 TYR cc_start: 0.8705 (m-80) cc_final: 0.8439 (m-80) REVERT: B 198 LEU cc_start: 0.9068 (mp) cc_final: 0.8828 (mm) REVERT: B 200 VAL cc_start: 0.8911 (p) cc_final: 0.8634 (m) REVERT: B 214 ARG cc_start: 0.7240 (ttp80) cc_final: 0.6976 (ttp80) REVERT: B 221 THR cc_start: 0.8316 (m) cc_final: 0.8002 (p) REVERT: B 254 ASP cc_start: 0.7149 (t0) cc_final: 0.6877 (t0) REVERT: B 277 SER cc_start: 0.8340 (t) cc_final: 0.8113 (t) REVERT: E 77 ASN cc_start: 0.8644 (t0) cc_final: 0.8429 (t0) REVERT: E 115 THR cc_start: 0.8008 (t) cc_final: 0.7600 (p) REVERT: E 202 ASP cc_start: 0.7416 (t70) cc_final: 0.7083 (t70) REVERT: E 232 GLN cc_start: 0.8429 (pp30) cc_final: 0.7873 (pp30) REVERT: M 200 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7879 (tt) REVERT: M 283 MET cc_start: 0.7854 (tpp) cc_final: 0.7629 (tpt) REVERT: M 312 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7957 (tm-30) REVERT: F 345 LYS cc_start: 0.8457 (tttt) cc_final: 0.8237 (tttp) REVERT: F 349 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7655 (mtmm) outliers start: 47 outliers final: 39 residues processed: 375 average time/residue: 0.2655 time to fit residues: 136.4433 Evaluate side-chains 388 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 345 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 317 THR Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain R residue 348 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 330 ASN Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 0.0770 chunk 129 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11984 Z= 0.173 Angle : 0.584 10.956 16305 Z= 0.289 Chirality : 0.040 0.184 1905 Planarity : 0.004 0.042 1964 Dihedral : 5.558 73.127 2245 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.25 % Allowed : 21.59 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.44 (0.22), residues: 1423 helix: 2.34 (0.19), residues: 649 sheet: 0.24 (0.30), residues: 307 loop : -0.51 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.017 0.001 PHE R 110 TYR 0.034 0.002 TYR A 290 ARG 0.009 0.001 ARG R 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 351 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8186 (mt) cc_final: 0.7870 (mt) REVERT: R 101 MET cc_start: 0.7039 (mtp) cc_final: 0.6780 (mtp) REVERT: R 221 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8653 (mp) REVERT: R 317 THR cc_start: 0.7633 (m) cc_final: 0.7370 (p) REVERT: A 14 GLU cc_start: 0.7291 (tt0) cc_final: 0.7054 (tt0) REVERT: A 17 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7840 (mtmm) REVERT: A 18 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6637 (tmm) REVERT: A 29 LYS cc_start: 0.8562 (tttt) cc_final: 0.8236 (ttmm) REVERT: A 33 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7090 (mt-10) REVERT: A 197 LYS cc_start: 0.8264 (mttt) cc_final: 0.7875 (mttt) REVERT: A 231 ASP cc_start: 0.7485 (t0) cc_final: 0.7186 (t0) REVERT: A 242 ARG cc_start: 0.7572 (ttm170) cc_final: 0.7213 (ttm170) REVERT: A 316 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 17 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 111 TYR cc_start: 0.8700 (m-80) cc_final: 0.8410 (m-80) REVERT: B 163 ASP cc_start: 0.8032 (p0) cc_final: 0.7733 (p0) REVERT: B 198 LEU cc_start: 0.9036 (mp) cc_final: 0.8810 (mm) REVERT: B 200 VAL cc_start: 0.8912 (p) cc_final: 0.8621 (m) REVERT: B 214 ARG cc_start: 0.7137 (ttp80) cc_final: 0.6901 (ttp80) REVERT: B 221 THR cc_start: 0.8284 (m) cc_final: 0.7991 (p) REVERT: B 254 ASP cc_start: 0.7149 (t0) cc_final: 0.6888 (t0) REVERT: B 277 SER cc_start: 0.8324 (t) cc_final: 0.8097 (t) REVERT: E 115 THR cc_start: 0.8079 (t) cc_final: 0.7643 (p) REVERT: E 202 ASP cc_start: 0.7415 (t70) cc_final: 0.7092 (t70) REVERT: E 214 THR cc_start: 0.7869 (m) cc_final: 0.7656 (t) REVERT: E 231 MET cc_start: 0.7605 (ttt) cc_final: 0.7333 (ttt) REVERT: E 232 GLN cc_start: 0.8399 (pp30) cc_final: 0.7891 (pp30) REVERT: M 200 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7884 (tt) REVERT: M 312 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8105 (tm-30) REVERT: F 345 LYS cc_start: 0.8461 (tttt) cc_final: 0.8240 (tttp) REVERT: F 349 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7654 (mtmm) outliers start: 41 outliers final: 36 residues processed: 370 average time/residue: 0.2701 time to fit residues: 136.2632 Evaluate side-chains 381 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 341 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 285 LEU Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11984 Z= 0.208 Angle : 0.613 12.310 16305 Z= 0.302 Chirality : 0.041 0.177 1905 Planarity : 0.004 0.042 1964 Dihedral : 5.676 73.853 2245 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.49 % Allowed : 21.43 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.33 (0.22), residues: 1423 helix: 2.28 (0.20), residues: 649 sheet: 0.21 (0.30), residues: 294 loop : -0.61 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE B 222 TYR 0.031 0.002 TYR R 130 ARG 0.010 0.001 ARG R 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 352 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 ILE cc_start: 0.8186 (mt) cc_final: 0.7879 (mt) REVERT: R 92 MET cc_start: 0.6671 (mmp) cc_final: 0.6218 (mmm) REVERT: R 101 MET cc_start: 0.7056 (mtp) cc_final: 0.6766 (mtp) REVERT: R 221 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8660 (mp) REVERT: A 14 GLU cc_start: 0.7301 (tt0) cc_final: 0.7085 (tt0) REVERT: A 17 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7790 (mtmm) REVERT: A 18 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6640 (tmm) REVERT: A 25 GLU cc_start: 0.7597 (tt0) cc_final: 0.7357 (tt0) REVERT: A 29 LYS cc_start: 0.8569 (tttt) cc_final: 0.8223 (ttmm) REVERT: A 33 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 197 LYS cc_start: 0.8295 (mttt) cc_final: 0.7931 (mttt) REVERT: A 231 ASP cc_start: 0.7467 (t0) cc_final: 0.7162 (t0) REVERT: A 242 ARG cc_start: 0.7501 (ttm170) cc_final: 0.7130 (ttm170) REVERT: A 316 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8076 (p) REVERT: A 330 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7972 (mmtt) REVERT: B 17 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 111 TYR cc_start: 0.8682 (m-80) cc_final: 0.8416 (m-80) REVERT: B 120 ILE cc_start: 0.8465 (mm) cc_final: 0.8262 (mm) REVERT: B 198 LEU cc_start: 0.9033 (mp) cc_final: 0.8725 (mm) REVERT: B 200 VAL cc_start: 0.8898 (p) cc_final: 0.8655 (m) REVERT: B 214 ARG cc_start: 0.7261 (ttp80) cc_final: 0.7034 (ttp80) REVERT: B 254 ASP cc_start: 0.7184 (t0) cc_final: 0.6969 (t0) REVERT: B 277 SER cc_start: 0.8233 (t) cc_final: 0.8017 (t) REVERT: E 115 THR cc_start: 0.8053 (t) cc_final: 0.7617 (p) REVERT: E 200 VAL cc_start: 0.9208 (t) cc_final: 0.8959 (m) REVERT: E 202 ASP cc_start: 0.7473 (t70) cc_final: 0.7172 (t70) REVERT: E 214 THR cc_start: 0.7951 (m) cc_final: 0.7708 (t) REVERT: E 231 MET cc_start: 0.7724 (ttt) cc_final: 0.7461 (ttt) REVERT: E 232 GLN cc_start: 0.8464 (pp30) cc_final: 0.7978 (pp30) REVERT: M 101 MET cc_start: 0.6155 (ttt) cc_final: 0.5859 (ttt) REVERT: M 200 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7918 (tt) REVERT: M 222 THR cc_start: 0.8703 (t) cc_final: 0.8410 (p) REVERT: F 345 LYS cc_start: 0.8478 (tttt) cc_final: 0.8249 (tttp) REVERT: F 349 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7670 (mtmm) outliers start: 44 outliers final: 36 residues processed: 374 average time/residue: 0.2585 time to fit residues: 133.0768 Evaluate side-chains 378 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 337 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain R residue 332 CYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 121 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 314 THR Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 340 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** M 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.106750 restraints weight = 20159.755| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.58 r_work: 0.3340 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11984 Z= 0.207 Angle : 0.614 13.294 16305 Z= 0.303 Chirality : 0.041 0.176 1905 Planarity : 0.004 0.042 1964 Dihedral : 5.733 75.549 2245 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.49 % Allowed : 21.98 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 1.29 (0.22), residues: 1423 helix: 2.24 (0.20), residues: 649 sheet: 0.26 (0.30), residues: 291 loop : -0.66 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.015 0.001 PHE E 204 TYR 0.022 0.002 TYR M 93 ARG 0.008 0.001 ARG R 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.51 seconds wall clock time: 60 minutes 27.03 seconds (3627.03 seconds total)