Starting phenix.real_space_refine on Thu Sep 26 01:30:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/09_2024/7o11_12686.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/09_2024/7o11_12686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/09_2024/7o11_12686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/09_2024/7o11_12686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/09_2024/7o11_12686.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o11_12686/09_2024/7o11_12686.cif" } resolution = 3.7 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= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 37 5.16 5 C 7466 2.51 5 N 2038 2.21 5 O 2109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3140 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain: "B" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2303 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 7.44, per 1000 atoms: 0.64 Number of scatterers: 11651 At special positions: 0 Unit cell: (87.21, 163.134, 137.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 Mg 1 11.99 O 2109 8.00 N 2038 7.00 C 7466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 45.4% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.735A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.625A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 removed outlier: 4.041A pdb=" N SER B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.679A pdb=" N ARG B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.607A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 removed outlier: 4.465A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.540A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.584A pdb=" N GLU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 243 removed outlier: 3.634A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.569A pdb=" N GLY B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.560A pdb=" N LEU B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 4.052A pdb=" N SER C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 107 through 113 removed outlier: 3.960A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.530A pdb=" N LEU C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.664A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 265 through 272 removed outlier: 3.726A pdb=" N ARG C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.651A pdb=" N LEU C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.083A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.622A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.569A pdb=" N ILE D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.507A pdb=" N TYR D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.876A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.072A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 146 through 167 removed outlier: 3.633A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 4.076A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.620A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 removed outlier: 3.504A pdb=" N LEU D 212 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.525A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 245 removed outlier: 3.769A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.629A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.511A pdb=" N ILE E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 7' Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.668A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.664A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.913A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.514A pdb=" N TYR E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.617A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.680A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.689A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.507A pdb=" N SER E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.631A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.528A pdb=" N LEU E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 removed outlier: 3.633A pdb=" N LEU E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.653A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 3.972A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 8.120A pdb=" N ARG A 44 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.542A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.207A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.417A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 7.542A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.607A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11 removed outlier: 7.401A pdb=" N GLN B 11 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N HIS B 20 " --> pdb=" O GLN B 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.669A pdb=" N LEU B 150 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 246 through 248 removed outlier: 4.120A pdb=" N SER B 246 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 226 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.558A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 11 removed outlier: 5.714A pdb=" N VAL C 9 " --> pdb=" O ASP C 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.994A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA C 198 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 209 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 200 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 254 through 259 removed outlier: 3.507A pdb=" N SER C 228 " --> pdb=" O ASP C 279 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1332 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: 4.01 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3104 1.33 - 1.45: 2076 1.45 - 1.57: 6625 1.57 - 1.69: 2 1.69 - 1.81: 64 Bond restraints: 11871 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.593 -0.068 2.10e-02 2.27e+03 1.04e+01 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.608 -0.068 2.70e-02 1.37e+03 6.32e+00 bond pdb=" CA ILE D 51 " pdb=" C ILE D 51 " ideal model delta sigma weight residual 1.523 1.543 -0.020 9.20e-03 1.18e+04 4.74e+00 bond pdb=" C LEU B 188 " pdb=" N PRO B 189 " ideal model delta sigma weight residual 1.333 1.356 -0.023 1.17e-02 7.31e+03 3.92e+00 bond pdb=" C ILE D 51 " pdb=" N PRO D 52 " ideal model delta sigma weight residual 1.337 1.358 -0.021 1.11e-02 8.12e+03 3.74e+00 ... (remaining 11866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 15879 3.78 - 7.55: 199 7.55 - 11.33: 30 11.33 - 15.10: 6 15.10 - 18.88: 2 Bond angle restraints: 16116 Sorted by residual: angle pdb=" CA LEU A 356 " pdb=" CB LEU A 356 " pdb=" CG LEU A 356 " ideal model delta sigma weight residual 116.30 135.18 -18.88 3.50e+00 8.16e-02 2.91e+01 angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 133.89 -17.59 3.50e+00 8.16e-02 2.53e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" CA GLU D 201 " pdb=" CB GLU D 201 " pdb=" CG GLU D 201 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 ... (remaining 16111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 6215 17.22 - 34.44: 643 34.44 - 51.65: 132 51.65 - 68.87: 23 68.87 - 86.09: 8 Dihedral angle restraints: 7021 sinusoidal: 2752 harmonic: 4269 Sorted by residual: dihedral pdb=" CA GLU B 276 " pdb=" C GLU B 276 " pdb=" N PRO B 277 " pdb=" CA PRO B 277 " ideal model delta harmonic sigma weight residual -180.00 -123.38 -56.62 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA ILE B 230 " pdb=" C ILE B 230 " pdb=" N SER B 231 " pdb=" CA SER B 231 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 7018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1672 0.100 - 0.200: 169 0.200 - 0.300: 17 0.300 - 0.400: 2 0.400 - 0.500: 1 Chirality restraints: 1861 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CB VAL C 187 " pdb=" CA VAL C 187 " pdb=" CG1 VAL C 187 " pdb=" CG2 VAL C 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASP A 182 " pdb=" N ASP A 182 " pdb=" C ASP A 182 " pdb=" CB ASP A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1858 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 276 " -0.064 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO B 277 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 30 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C VAL D 30 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL D 30 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU D 31 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.050 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO D 67 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.042 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 116 2.55 - 3.14: 7928 3.14 - 3.72: 18612 3.72 - 4.31: 26243 4.31 - 4.90: 42841 Nonbonded interactions: 95740 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 1.960 2.170 nonbonded pdb=" OD1 ASP A 363 " pdb="MG MG A 501 " model vdw 2.156 2.170 nonbonded pdb=" OD1 ASN A 361 " pdb="MG MG A 501 " model vdw 2.321 2.170 nonbonded pdb=" OG SER C 286 " pdb=" OE1 GLU C 288 " model vdw 2.324 3.040 nonbonded pdb=" O SER B 90 " pdb=" OG1 THR B 94 " model vdw 2.340 3.040 ... (remaining 95735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 2 through 299) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.650 Find NCS groups from input model: 0.370 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.006 0.075 11871 Z= 0.387 Angle : 1.107 18.875 16116 Z= 0.570 Chirality : 0.063 0.500 1861 Planarity : 0.007 0.096 2063 Dihedral : 14.722 86.089 4299 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.74 % Allowed : 9.40 % Favored : 89.87 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -5.78 (0.15), residues: 1498 helix: -4.54 (0.07), residues: 654 sheet: -3.49 (0.28), residues: 199 loop : -2.94 (0.20), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 45 HIS 0.010 0.002 HIS A 163 PHE 0.020 0.002 PHE E 64 TYR 0.019 0.002 TYR A 204 ARG 0.004 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8011 (pt) cc_final: 0.7765 (pp) REVERT: A 106 ASP cc_start: 0.7100 (m-30) cc_final: 0.6653 (m-30) REVERT: A 125 MET cc_start: 0.9202 (mpp) cc_final: 0.8972 (mpp) REVERT: A 235 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9298 (tppp) REVERT: A 305 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8647 (mtmt) REVERT: B 2 ASN cc_start: 0.8674 (m110) cc_final: 0.7991 (m-40) REVERT: B 46 MET cc_start: 0.9111 (ttp) cc_final: 0.8536 (ttp) REVERT: B 86 TYR cc_start: 0.9025 (m-80) cc_final: 0.8815 (m-10) REVERT: B 131 LYS cc_start: 0.9598 (tptt) cc_final: 0.9309 (tppt) REVERT: B 263 HIS cc_start: 0.8689 (m90) cc_final: 0.8440 (m90) REVERT: B 281 GLU cc_start: 0.8886 (pt0) cc_final: 0.8433 (pm20) REVERT: C 133 MET cc_start: 0.9103 (mtm) cc_final: 0.8635 (mtm) REVERT: D 9 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8331 (mtm180) REVERT: D 11 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7709 (mm-30) REVERT: D 66 MET cc_start: 0.9056 (mmm) cc_final: 0.8800 (mmp) REVERT: D 201 GLU cc_start: 0.8077 (pm20) cc_final: 0.7869 (pm20) REVERT: D 203 LYS cc_start: 0.9039 (mttt) cc_final: 0.8516 (pptt) REVERT: D 216 ASN cc_start: 0.8789 (t0) cc_final: 0.8188 (t0) REVERT: E 3 GLN cc_start: 0.8360 (mt0) cc_final: 0.8053 (mt0) REVERT: E 20 TRP cc_start: 0.8844 (m100) cc_final: 0.8348 (m-10) REVERT: E 81 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7660 (mt-10) REVERT: E 138 MET cc_start: 0.7566 (tpt) cc_final: 0.7179 (tmm) outliers start: 9 outliers final: 2 residues processed: 162 average time/residue: 0.2472 time to fit residues: 57.1821 Evaluate side-chains 103 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 0.0000 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 190 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 417 HIS B 20 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 214 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 97 HIS C 214 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN E 108 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11871 Z= 0.208 Angle : 0.631 10.866 16116 Z= 0.321 Chirality : 0.043 0.166 1861 Planarity : 0.005 0.099 2063 Dihedral : 5.387 47.352 1644 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.14 % Allowed : 13.97 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -3.65 (0.18), residues: 1498 helix: -1.99 (0.16), residues: 664 sheet: -3.13 (0.30), residues: 198 loop : -2.50 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.004 0.001 HIS B 37 PHE 0.012 0.001 PHE E 157 TYR 0.020 0.002 TYR C 13 ARG 0.005 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.9119 (mpp) cc_final: 0.8854 (mpp) REVERT: A 231 MET cc_start: 0.8318 (mtt) cc_final: 0.7997 (mtp) REVERT: A 235 LYS cc_start: 0.9538 (mmmt) cc_final: 0.9333 (tppp) REVERT: A 305 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8786 (mtmt) REVERT: B 2 ASN cc_start: 0.8507 (m110) cc_final: 0.8095 (m-40) REVERT: B 263 HIS cc_start: 0.8728 (m90) cc_final: 0.8462 (m90) REVERT: C 133 MET cc_start: 0.9127 (mtm) cc_final: 0.8717 (mtm) REVERT: D 11 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8253 (mm-30) REVERT: D 82 ASP cc_start: 0.9039 (t0) cc_final: 0.8768 (t0) REVERT: D 83 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8680 (mm-30) REVERT: D 203 LYS cc_start: 0.9077 (mttt) cc_final: 0.8617 (pptt) REVERT: D 216 ASN cc_start: 0.8621 (t0) cc_final: 0.7513 (t0) REVERT: D 219 ASP cc_start: 0.8936 (m-30) cc_final: 0.8639 (m-30) REVERT: E 20 TRP cc_start: 0.8785 (m100) cc_final: 0.8444 (m-10) REVERT: E 138 MET cc_start: 0.7427 (tpt) cc_final: 0.7175 (tmm) REVERT: E 187 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8782 (pp) REVERT: E 211 TRP cc_start: 0.7759 (m-10) cc_final: 0.6775 (t60) outliers start: 14 outliers final: 6 residues processed: 129 average time/residue: 0.2459 time to fit residues: 46.3175 Evaluate side-chains 103 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 111 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 119 optimal weight: 0.3980 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11871 Z= 0.191 Angle : 0.595 9.300 16116 Z= 0.296 Chirality : 0.042 0.164 1861 Planarity : 0.004 0.097 2063 Dihedral : 4.987 44.023 1643 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.23 % Allowed : 16.42 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1498 helix: -0.41 (0.20), residues: 668 sheet: -2.87 (0.31), residues: 200 loop : -2.28 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.003 0.001 HIS B 37 PHE 0.011 0.001 PHE E 157 TYR 0.020 0.001 TYR C 13 ARG 0.004 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.9043 (mpp) cc_final: 0.8774 (mpp) REVERT: A 231 MET cc_start: 0.8346 (mtt) cc_final: 0.7987 (mtp) REVERT: A 305 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8749 (mtmt) REVERT: B 2 ASN cc_start: 0.8515 (m110) cc_final: 0.8109 (m-40) REVERT: B 86 TYR cc_start: 0.9107 (m-80) cc_final: 0.8794 (m-80) REVERT: B 263 HIS cc_start: 0.8727 (m90) cc_final: 0.8431 (m90) REVERT: C 61 LYS cc_start: 0.8710 (mttm) cc_final: 0.8285 (mmmt) REVERT: C 133 MET cc_start: 0.9052 (mtm) cc_final: 0.8833 (mtm) REVERT: D 82 ASP cc_start: 0.9024 (t0) cc_final: 0.8734 (t0) REVERT: D 83 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8579 (mm-30) REVERT: D 203 LYS cc_start: 0.9169 (mttt) cc_final: 0.8736 (pptt) REVERT: D 216 ASN cc_start: 0.8608 (t0) cc_final: 0.7511 (t0) REVERT: D 219 ASP cc_start: 0.8930 (m-30) cc_final: 0.8602 (m-30) REVERT: D 230 GLU cc_start: 0.7899 (mp0) cc_final: 0.7676 (mp0) REVERT: E 20 TRP cc_start: 0.8753 (m100) cc_final: 0.8520 (m-10) REVERT: E 27 LEU cc_start: 0.9112 (tt) cc_final: 0.8395 (mm) REVERT: E 93 TYR cc_start: 0.9051 (m-80) cc_final: 0.8842 (m-80) REVERT: E 138 MET cc_start: 0.7358 (tpt) cc_final: 0.7154 (tmm) REVERT: E 187 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8787 (pp) REVERT: E 211 TRP cc_start: 0.7802 (m-10) cc_final: 0.6771 (t60) outliers start: 15 outliers final: 8 residues processed: 117 average time/residue: 0.2476 time to fit residues: 43.5532 Evaluate side-chains 103 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 0.0370 chunk 14 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 6 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11871 Z= 0.158 Angle : 0.578 9.785 16116 Z= 0.281 Chirality : 0.042 0.221 1861 Planarity : 0.004 0.095 2063 Dihedral : 4.777 42.995 1643 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.04 % Allowed : 17.57 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.63 (0.22), residues: 1498 helix: 0.35 (0.21), residues: 662 sheet: -2.62 (0.32), residues: 212 loop : -2.05 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 98 HIS 0.003 0.001 HIS B 37 PHE 0.010 0.001 PHE E 157 TYR 0.024 0.001 TYR C 13 ARG 0.005 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 231 MET cc_start: 0.8431 (mtt) cc_final: 0.8087 (mtp) REVERT: A 299 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: A 305 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8728 (mtmt) REVERT: B 2 ASN cc_start: 0.8486 (m110) cc_final: 0.8126 (m-40) REVERT: B 46 MET cc_start: 0.8667 (ttp) cc_final: 0.8457 (tpp) REVERT: B 263 HIS cc_start: 0.8735 (m90) cc_final: 0.8498 (m170) REVERT: C 61 LYS cc_start: 0.8762 (mttm) cc_final: 0.8299 (mmmt) REVERT: D 64 PHE cc_start: 0.8905 (m-80) cc_final: 0.8687 (m-80) REVERT: D 75 TYR cc_start: 0.9235 (p90) cc_final: 0.9018 (p90) REVERT: D 81 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8240 (mt-10) REVERT: D 82 ASP cc_start: 0.9003 (t0) cc_final: 0.8640 (t0) REVERT: D 83 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8565 (mm-30) REVERT: D 203 LYS cc_start: 0.9100 (mttt) cc_final: 0.8659 (pptt) REVERT: D 216 ASN cc_start: 0.8570 (t0) cc_final: 0.7446 (t0) REVERT: D 219 ASP cc_start: 0.8912 (m-30) cc_final: 0.8576 (m-30) REVERT: E 3 GLN cc_start: 0.8527 (mt0) cc_final: 0.8054 (tt0) REVERT: E 20 TRP cc_start: 0.8839 (m100) cc_final: 0.8638 (m-10) REVERT: E 138 MET cc_start: 0.7372 (tpt) cc_final: 0.7157 (tmm) REVERT: E 187 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8758 (pp) REVERT: E 211 TRP cc_start: 0.7773 (m-10) cc_final: 0.6759 (t60) outliers start: 25 outliers final: 13 residues processed: 129 average time/residue: 0.2554 time to fit residues: 48.7801 Evaluate side-chains 113 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 59 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 128 optimal weight: 0.0170 chunk 36 optimal weight: 6.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11871 Z= 0.157 Angle : 0.564 9.562 16116 Z= 0.274 Chirality : 0.041 0.163 1861 Planarity : 0.004 0.094 2063 Dihedral : 4.616 42.472 1643 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.04 % Allowed : 17.97 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1498 helix: 0.82 (0.22), residues: 660 sheet: -2.34 (0.33), residues: 208 loop : -1.96 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 400 HIS 0.002 0.001 HIS B 186 PHE 0.011 0.001 PHE E 157 TYR 0.026 0.001 TYR C 13 ARG 0.005 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7920 (pp) REVERT: A 305 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8727 (mtmt) REVERT: B 2 ASN cc_start: 0.8455 (m110) cc_final: 0.8120 (m-40) REVERT: B 263 HIS cc_start: 0.8700 (m90) cc_final: 0.8490 (m170) REVERT: C 61 LYS cc_start: 0.8803 (mttm) cc_final: 0.8323 (mmmt) REVERT: D 82 ASP cc_start: 0.9049 (t0) cc_final: 0.8709 (t0) REVERT: D 83 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8554 (mm-30) REVERT: D 203 LYS cc_start: 0.9011 (mttt) cc_final: 0.8656 (pptt) REVERT: D 216 ASN cc_start: 0.8630 (t0) cc_final: 0.7526 (t0) REVERT: D 219 ASP cc_start: 0.8884 (m-30) cc_final: 0.8524 (m-30) REVERT: E 3 GLN cc_start: 0.8467 (mt0) cc_final: 0.8079 (tt0) REVERT: E 211 TRP cc_start: 0.7741 (m-10) cc_final: 0.6747 (t60) outliers start: 25 outliers final: 19 residues processed: 127 average time/residue: 0.2240 time to fit residues: 42.3403 Evaluate side-chains 115 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 0.0370 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11871 Z= 0.169 Angle : 0.590 12.186 16116 Z= 0.282 Chirality : 0.042 0.288 1861 Planarity : 0.004 0.093 2063 Dihedral : 4.578 42.124 1643 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.45 % Allowed : 19.20 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -1.01 (0.23), residues: 1498 helix: 1.03 (0.22), residues: 661 sheet: -2.26 (0.34), residues: 209 loop : -1.97 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.008 0.001 HIS B 283 PHE 0.013 0.001 PHE D 64 TYR 0.029 0.001 TYR C 13 ARG 0.004 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 299 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: A 305 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8732 (mtmt) REVERT: B 2 ASN cc_start: 0.8433 (m110) cc_final: 0.8117 (m-40) REVERT: B 86 TYR cc_start: 0.9029 (m-80) cc_final: 0.8715 (m-80) REVERT: C 61 LYS cc_start: 0.8805 (mttm) cc_final: 0.8326 (mmmt) REVERT: D 82 ASP cc_start: 0.9025 (t0) cc_final: 0.8692 (t0) REVERT: D 83 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8539 (mm-30) REVERT: D 203 LYS cc_start: 0.9026 (mttt) cc_final: 0.8654 (pptt) REVERT: D 216 ASN cc_start: 0.8663 (t0) cc_final: 0.7534 (t0) REVERT: D 219 ASP cc_start: 0.8890 (m-30) cc_final: 0.8523 (m-30) REVERT: E 3 GLN cc_start: 0.8494 (mt0) cc_final: 0.8137 (tt0) REVERT: E 187 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8740 (pp) REVERT: E 211 TRP cc_start: 0.7702 (m-10) cc_final: 0.6724 (t60) outliers start: 30 outliers final: 17 residues processed: 121 average time/residue: 0.2186 time to fit residues: 39.3338 Evaluate side-chains 117 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 261 ASN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11871 Z= 0.206 Angle : 0.588 10.465 16116 Z= 0.285 Chirality : 0.043 0.194 1861 Planarity : 0.004 0.093 2063 Dihedral : 4.560 41.715 1643 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.21 % Allowed : 19.53 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -0.85 (0.23), residues: 1498 helix: 1.22 (0.22), residues: 664 sheet: -2.19 (0.33), residues: 213 loop : -1.95 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 400 HIS 0.004 0.001 HIS B 186 PHE 0.010 0.001 PHE E 157 TYR 0.030 0.001 TYR C 13 ARG 0.004 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: A 305 LYS cc_start: 0.9144 (mmtt) cc_final: 0.8700 (mtmt) REVERT: B 2 ASN cc_start: 0.8451 (m110) cc_final: 0.8133 (m-40) REVERT: B 86 TYR cc_start: 0.9036 (m-80) cc_final: 0.8671 (m-80) REVERT: C 61 LYS cc_start: 0.8827 (mttm) cc_final: 0.8331 (mmmt) REVERT: D 82 ASP cc_start: 0.9019 (t0) cc_final: 0.8680 (t0) REVERT: D 83 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8795 (mm-30) REVERT: D 203 LYS cc_start: 0.9058 (mttt) cc_final: 0.8661 (pptt) REVERT: D 216 ASN cc_start: 0.8690 (t0) cc_final: 0.7545 (t0) REVERT: D 219 ASP cc_start: 0.8915 (m-30) cc_final: 0.8547 (m-30) REVERT: E 3 GLN cc_start: 0.8507 (mt0) cc_final: 0.8125 (tt0) REVERT: E 187 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8762 (pp) REVERT: E 211 TRP cc_start: 0.7714 (m-10) cc_final: 0.6751 (t60) outliers start: 27 outliers final: 22 residues processed: 118 average time/residue: 0.2216 time to fit residues: 38.8499 Evaluate side-chains 118 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 0.3980 chunk 129 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11871 Z= 0.217 Angle : 0.604 11.580 16116 Z= 0.292 Chirality : 0.043 0.195 1861 Planarity : 0.004 0.092 2063 Dihedral : 4.566 41.571 1643 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.29 % Allowed : 20.02 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -0.71 (0.23), residues: 1498 helix: 1.34 (0.22), residues: 666 sheet: -2.19 (0.34), residues: 215 loop : -1.88 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 400 HIS 0.004 0.001 HIS B 186 PHE 0.011 0.001 PHE D 157 TYR 0.031 0.001 TYR C 13 ARG 0.004 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 142 VAL cc_start: 0.9428 (OUTLIER) cc_final: 0.9066 (p) REVERT: A 305 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8710 (mtmt) REVERT: B 2 ASN cc_start: 0.8434 (m110) cc_final: 0.8154 (m-40) REVERT: C 61 LYS cc_start: 0.8830 (mttm) cc_final: 0.8325 (mmmt) REVERT: D 82 ASP cc_start: 0.9003 (t0) cc_final: 0.8653 (t0) REVERT: D 83 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8804 (mm-30) REVERT: D 201 GLU cc_start: 0.8537 (pm20) cc_final: 0.8268 (pm20) REVERT: D 203 LYS cc_start: 0.9066 (mttt) cc_final: 0.8663 (pptt) REVERT: D 216 ASN cc_start: 0.8719 (t0) cc_final: 0.7866 (t0) REVERT: E 3 GLN cc_start: 0.8468 (mt0) cc_final: 0.8082 (tt0) REVERT: E 187 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8780 (pp) REVERT: E 211 TRP cc_start: 0.7740 (m-10) cc_final: 0.6708 (t60) outliers start: 28 outliers final: 23 residues processed: 118 average time/residue: 0.2259 time to fit residues: 39.6732 Evaluate side-chains 122 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 261 ASN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11871 Z= 0.213 Angle : 0.599 11.992 16116 Z= 0.291 Chirality : 0.042 0.190 1861 Planarity : 0.004 0.092 2063 Dihedral : 4.550 41.182 1643 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.29 % Allowed : 20.18 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -0.64 (0.23), residues: 1498 helix: 1.40 (0.22), residues: 666 sheet: -2.20 (0.34), residues: 215 loop : -1.83 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 400 HIS 0.004 0.001 HIS B 194 PHE 0.011 0.001 PHE E 157 TYR 0.031 0.001 TYR C 13 ARG 0.006 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8712 (mtmt) REVERT: B 2 ASN cc_start: 0.8431 (m110) cc_final: 0.8152 (m-40) REVERT: B 86 TYR cc_start: 0.9048 (m-80) cc_final: 0.8713 (m-80) REVERT: C 61 LYS cc_start: 0.8833 (mttm) cc_final: 0.8323 (mmmt) REVERT: C 224 ARG cc_start: 0.8335 (tmt170) cc_final: 0.8095 (tmt170) REVERT: D 81 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8165 (mt-10) REVERT: D 82 ASP cc_start: 0.8994 (t0) cc_final: 0.8642 (t0) REVERT: D 83 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8828 (mm-30) REVERT: D 201 GLU cc_start: 0.8557 (pm20) cc_final: 0.8288 (pm20) REVERT: D 203 LYS cc_start: 0.9069 (mttt) cc_final: 0.8663 (pptt) REVERT: D 216 ASN cc_start: 0.8775 (t0) cc_final: 0.7682 (t0) REVERT: D 219 ASP cc_start: 0.8928 (m-30) cc_final: 0.8512 (m-30) REVERT: E 66 MET cc_start: 0.9109 (tpp) cc_final: 0.8847 (mmp) REVERT: E 187 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8794 (pp) REVERT: E 211 TRP cc_start: 0.7643 (m-10) cc_final: 0.6687 (t60) outliers start: 28 outliers final: 26 residues processed: 117 average time/residue: 0.2282 time to fit residues: 39.6940 Evaluate side-chains 122 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11871 Z= 0.237 Angle : 0.618 13.020 16116 Z= 0.299 Chirality : 0.043 0.181 1861 Planarity : 0.004 0.092 2063 Dihedral : 4.558 41.048 1643 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.21 % Allowed : 20.34 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1498 helix: 1.43 (0.22), residues: 666 sheet: -2.19 (0.34), residues: 215 loop : -1.80 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 400 HIS 0.006 0.001 HIS B 283 PHE 0.011 0.001 PHE D 157 TYR 0.031 0.002 TYR C 13 ARG 0.004 0.000 ARG C 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 2.077 Fit side-chains revert: symmetry clash REVERT: A 305 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8700 (mtmt) REVERT: B 2 ASN cc_start: 0.8397 (m110) cc_final: 0.8101 (m-40) REVERT: B 86 TYR cc_start: 0.9057 (m-80) cc_final: 0.8721 (m-80) REVERT: C 61 LYS cc_start: 0.8839 (mttm) cc_final: 0.8323 (mmmt) REVERT: D 81 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8187 (mt-10) REVERT: D 82 ASP cc_start: 0.9043 (t0) cc_final: 0.8645 (t0) REVERT: D 83 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8605 (mm-30) REVERT: D 201 GLU cc_start: 0.8571 (pm20) cc_final: 0.8303 (pm20) REVERT: D 203 LYS cc_start: 0.9075 (mttt) cc_final: 0.8685 (pptt) REVERT: D 216 ASN cc_start: 0.8773 (t0) cc_final: 0.7679 (t0) REVERT: D 219 ASP cc_start: 0.8937 (m-30) cc_final: 0.8517 (m-30) REVERT: E 66 MET cc_start: 0.9110 (tpp) cc_final: 0.8845 (mmp) REVERT: E 187 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8791 (pp) REVERT: E 211 TRP cc_start: 0.7690 (m-10) cc_final: 0.6678 (t60) outliers start: 27 outliers final: 25 residues processed: 117 average time/residue: 0.2365 time to fit residues: 42.5404 Evaluate side-chains 122 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 255 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 37 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.055803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.044592 restraints weight = 55400.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046024 restraints weight = 28013.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.046873 restraints weight = 18064.008| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11871 Z= 0.283 Angle : 0.648 13.273 16116 Z= 0.315 Chirality : 0.044 0.180 1861 Planarity : 0.004 0.091 2063 Dihedral : 4.664 41.145 1643 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.29 % Allowed : 20.34 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -0.60 (0.23), residues: 1498 helix: 1.41 (0.22), residues: 667 sheet: -2.18 (0.34), residues: 215 loop : -1.77 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 37 HIS 0.006 0.001 HIS B 186 PHE 0.013 0.001 PHE E 204 TYR 0.029 0.002 TYR C 13 ARG 0.005 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2138.14 seconds wall clock time: 40 minutes 28.85 seconds (2428.85 seconds total)