Starting phenix.real_space_refine on Fri Sep 27 15:21:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwv_27761/09_2024/8dwv_27761.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwv_27761/09_2024/8dwv_27761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwv_27761/09_2024/8dwv_27761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwv_27761/09_2024/8dwv_27761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwv_27761/09_2024/8dwv_27761.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwv_27761/09_2024/8dwv_27761.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.057 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 150 5.16 5 C 10450 2.51 5 N 2744 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 353, 2780 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 339} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 346, 2741 Classifications: {'peptide': 346} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 335} Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 349, 2754 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2749 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 347, 2749 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 336} Chain: "G" Number of atoms: 2737 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 345, 2737 Classifications: {'peptide': 345} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 334} Chain: "H" Number of atoms: 2719 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2719 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 9.51, per 1000 atoms: 0.58 Number of scatterers: 16480 At special positions: 0 Unit cell: (74.6929, 139.521, 305.818, 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 150 16.00 O 3136 8.00 N 2744 7.00 C 10450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 361 " - pdb=" SG CYS H 361 " distance=2.03 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: 3.56 Conformation dependent library (CDL) restraints added in 1.9 seconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4004 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 44.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 185 through 197 removed outlier: 3.588A pdb=" N LEU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.133A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.514A pdb=" N GLU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.168A pdb=" N SER A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 4.502A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.604A pdb=" N MET A 269 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 270 " --> pdb=" O ASP A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.617A pdb=" N ILE A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 333 removed outlier: 6.319A pdb=" N SER A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.699A pdb=" N LYS A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.772A pdb=" N SER A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.756A pdb=" N ASP B 63 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 145 through 148 Processing helix chain 'B' and resid 185 through 197 Processing helix chain 'B' and resid 214 through 222 removed outlier: 3.552A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.548A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.513A pdb=" N SER B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.226A pdb=" N VAL B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.787A pdb=" N VAL B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 removed outlier: 3.541A pdb=" N LYS E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 145 through 148 Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.542A pdb=" N GLY E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.572A pdb=" N HIS E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 255 removed outlier: 4.416A pdb=" N GLU E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.516A pdb=" N LEU E 273 " --> pdb=" O MET E 269 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 328 through 333 removed outlier: 4.189A pdb=" N LEU E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.596A pdb=" N LYS E 339 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 360 removed outlier: 3.711A pdb=" N VAL E 349 " --> pdb=" O HIS E 345 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 358 " --> pdb=" O ARG E 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.926A pdb=" N ASP F 63 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 4.265A pdb=" N LYS F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.601A pdb=" N ASP F 153 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 197 Processing helix chain 'F' and resid 215 through 222 Processing helix chain 'F' and resid 222 through 228 removed outlier: 3.734A pdb=" N MET F 228 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 247 through 261 Processing helix chain 'F' and resid 266 through 268 No H-bonds generated for 'chain 'F' and resid 266 through 268' Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 284 through 295 removed outlier: 3.618A pdb=" N SER F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 315 through 333 removed outlier: 6.059A pdb=" N SER F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP F 331 " --> pdb=" O TYR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.716A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 358 removed outlier: 3.508A pdb=" N VAL F 349 " --> pdb=" O HIS F 345 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 358 " --> pdb=" O ARG F 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.666A pdb=" N ARG G 45 " --> pdb=" O PHE G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 removed outlier: 4.197A pdb=" N ASP G 82 " --> pdb=" O GLU G 78 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 150 through 154 Processing helix chain 'G' and resid 185 through 197 removed outlier: 4.201A pdb=" N GLU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 Processing helix chain 'G' and resid 222 through 230 removed outlier: 3.956A pdb=" N MET G 228 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE G 229 " --> pdb=" O PHE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 Processing helix chain 'G' and resid 247 through 260 Processing helix chain 'G' and resid 266 through 268 No H-bonds generated for 'chain 'G' and resid 266 through 268' Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 282 through 295 removed outlier: 3.735A pdb=" N SER G 295 " --> pdb=" O ASP G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 314 through 333 removed outlier: 6.168A pdb=" N SER G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP G 331 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 removed outlier: 4.288A pdb=" N LYS G 339 " --> pdb=" O THR G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.580A pdb=" N VAL G 349 " --> pdb=" O HIS G 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 44 Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 150 through 154 Processing helix chain 'H' and resid 185 through 192 removed outlier: 3.714A pdb=" N GLU H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 4.017A pdb=" N ASN H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 221 removed outlier: 3.982A pdb=" N LEU H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.755A pdb=" N HIS H 231 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.737A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 269 through 281 Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.739A pdb=" N SER H 295 " --> pdb=" O ASP H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 313 Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 328 through 333 removed outlier: 4.087A pdb=" N LEU H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 345 Processing helix chain 'H' and resid 345 through 359 removed outlier: 3.511A pdb=" N VAL H 349 " --> pdb=" O HIS H 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 38 removed outlier: 3.564A pdb=" N PHE A 32 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 34 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS A 159 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 36 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 155 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR A 156 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 72 removed outlier: 6.412A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 72 removed outlier: 6.412A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 137 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 209 through 213 removed outlier: 8.393A pdb=" N ILE A 243 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS A 205 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.628A pdb=" N ILE B 137 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU B 86 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS B 135 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 213 removed outlier: 4.095A pdb=" N VAL B 241 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 205 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 29 through 38 removed outlier: 4.962A pdb=" N THR E 156 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 115 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 66 through 72 removed outlier: 7.015A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N AARG E 70 " --> pdb=" O TYR E 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AB3, first strand: chain 'E' and resid 202 through 206 removed outlier: 4.020A pdb=" N PHE E 211 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.791A pdb=" N VAL F 164 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG F 99 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 68 through 72 removed outlier: 3.760A pdb=" N ASN F 72 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER F 85 " --> pdb=" O ASN F 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 105 Processing sheet with id=AB7, first strand: chain 'F' and resid 205 through 206 Processing sheet with id=AB8, first strand: chain 'G' and resid 29 through 38 removed outlier: 3.948A pdb=" N CYS G 159 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP G 36 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE G 38 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 155 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G 99 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.911A pdb=" N VAL G 71 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS G 66 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N AARG G 70 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER G 85 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU G 86 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE G 133 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AC2, first strand: chain 'H' and resid 29 through 35 Processing sheet with id=AC3, first strand: chain 'H' and resid 67 through 71 removed outlier: 3.573A pdb=" N TYR H 87 " --> pdb=" O AARG H 70 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU H 86 " --> pdb=" O LYS H 135 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LYS H 135 " --> pdb=" O LEU H 86 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N LEU H 88 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N PHE H 133 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU H 90 " --> pdb=" O TRP H 131 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TRP H 131 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AC5, first strand: chain 'H' and resid 103 through 107 removed outlier: 3.597A pdb=" N LYS H 115 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 205 through 206 639 hydrogen bonds defined for protein. 1773 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: 4.63 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5371 1.35 - 1.47: 3829 1.47 - 1.59: 7384 1.59 - 1.71: 0 1.71 - 1.83: 222 Bond restraints: 16806 Sorted by residual: bond pdb=" N GLN G 173 " pdb=" CA GLN G 173 " ideal model delta sigma weight residual 1.457 1.505 -0.047 1.29e-02 6.01e+03 1.35e+01 bond pdb=" N SER G 171 " pdb=" CA SER G 171 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.36e+00 bond pdb=" N ILE G 170 " pdb=" CA ILE G 170 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.30e-02 5.92e+03 7.58e+00 bond pdb=" N GLU E 46 " pdb=" CA GLU E 46 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.35e+00 bond pdb=" N VAL G 168 " pdb=" CA VAL G 168 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.95e+00 ... (remaining 16801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 22435 3.08 - 6.15: 212 6.15 - 9.23: 16 9.23 - 12.31: 1 12.31 - 15.38: 1 Bond angle restraints: 22665 Sorted by residual: angle pdb=" C MET B 176 " pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 123.91 139.29 -15.38 1.66e+00 3.63e-01 8.59e+01 angle pdb=" O PHE E 43 " pdb=" C PHE E 43 " pdb=" N CYS E 44 " ideal model delta sigma weight residual 122.32 129.03 -6.71 1.15e+00 7.56e-01 3.40e+01 angle pdb=" CA PHE E 43 " pdb=" C PHE E 43 " pdb=" N CYS E 44 " ideal model delta sigma weight residual 117.07 110.83 6.24 1.21e+00 6.83e-01 2.66e+01 angle pdb=" CA ILE G 170 " pdb=" C ILE G 170 " pdb=" O ILE G 170 " ideal model delta sigma weight residual 121.58 116.63 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" N GLN G 173 " pdb=" CA GLN G 173 " pdb=" CB GLN G 173 " ideal model delta sigma weight residual 110.49 118.61 -8.12 1.69e+00 3.50e-01 2.31e+01 ... (remaining 22660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 9257 17.89 - 35.79: 761 35.79 - 53.68: 154 53.68 - 71.58: 34 71.58 - 89.47: 19 Dihedral angle restraints: 10225 sinusoidal: 4089 harmonic: 6136 Sorted by residual: dihedral pdb=" CA VAL G 168 " pdb=" C VAL G 168 " pdb=" N ASN G 169 " pdb=" CA ASN G 169 " ideal model delta harmonic sigma weight residual -180.00 -108.12 -71.88 0 5.00e+00 4.00e-02 2.07e+02 dihedral pdb=" CB CYS F 361 " pdb=" SG CYS F 361 " pdb=" SG CYS H 361 " pdb=" CB CYS H 361 " ideal model delta sinusoidal sigma weight residual -86.00 -173.37 87.37 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CA SER G 171 " pdb=" C SER G 171 " pdb=" N GLY G 172 " pdb=" CA GLY G 172 " ideal model delta harmonic sigma weight residual 0.00 -41.89 41.89 0 5.00e+00 4.00e-02 7.02e+01 ... (remaining 10222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2364 0.095 - 0.191: 125 0.191 - 0.286: 2 0.286 - 0.381: 3 0.381 - 0.477: 2 Chirality restraints: 2496 Sorted by residual: chirality pdb=" CA ARG E 198 " pdb=" N ARG E 198 " pdb=" C ARG E 198 " pdb=" CB ARG E 198 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ARG E 45 " pdb=" N ARG E 45 " pdb=" C ARG E 45 " pdb=" CB ARG E 45 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 2493 not shown) Planarity restraints: 2911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 164 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C VAL G 164 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL G 164 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN G 165 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 361 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO F 362 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO F 362 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 362 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 43 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.72e+00 pdb=" C PHE E 43 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE E 43 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS E 44 " 0.011 2.00e-02 2.50e+03 ... (remaining 2908 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 241 2.64 - 3.21: 15787 3.21 - 3.77: 24564 3.77 - 4.34: 32439 4.34 - 4.90: 53679 Nonbonded interactions: 126710 Sorted by model distance: nonbonded pdb=" OG1 THR G 25 " pdb=" O THR H 37 " model vdw 2.076 3.040 nonbonded pdb=" O LEU E 76 " pdb=" OG SER E 80 " model vdw 2.081 3.040 nonbonded pdb=" OG SER G 298 " pdb=" OD1 ASN G 301 " model vdw 2.085 3.040 nonbonded pdb=" O LEU H 218 " pdb=" OG SER H 222 " model vdw 2.100 3.040 nonbonded pdb=" OG SER G 42 " pdb=" OD2 ASP G 153 " model vdw 2.108 3.040 ... (remaining 126705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) selection = (chain 'B' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'E' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 361)) selection = (chain 'F' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'G' and (resid 20 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 248 or (resid 249 and (name N o \ r name CA or name C or name O or name CB )) or resid 250 through 361)) selection = (chain 'H' and (resid 20 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 250 through 361)) } 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.470 Find NCS groups from input model: 0.840 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4687 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 0.047 16806 Z= 0.247 Angle : 0.740 15.384 22665 Z= 0.405 Chirality : 0.046 0.477 2496 Planarity : 0.004 0.072 2911 Dihedral : 14.514 89.471 6218 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.83 % Favored : 90.59 % Rotamer: Outliers : 0.28 % Allowed : 0.06 % Favored : 99.67 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.14 (0.19), residues: 2072 helix: 0.86 (0.20), residues: 717 sheet: -1.10 (0.30), residues: 296 loop : -1.86 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 67 HIS 0.004 0.001 HIS B 214 PHE 0.022 0.002 PHE F 43 TYR 0.014 0.001 TYR E 327 ARG 0.006 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.2263 (tpt) cc_final: 0.1152 (tpt) REVERT: B 48 MET cc_start: 0.2399 (pmm) cc_final: 0.1542 (ppp) REVERT: B 176 MET cc_start: 0.6608 (tmm) cc_final: 0.5254 (mpp) REVERT: H 288 MET cc_start: 0.6949 (ppp) cc_final: 0.6560 (ppp) outliers start: 5 outliers final: 4 residues processed: 119 average time/residue: 0.2754 time to fit residues: 50.8491 Evaluate side-chains 98 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 173 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 62 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 62 ASN A 196 ASN B 239 ASN B 312 HIS E 62 ASN E 328 HIS E 347 HIS E 360 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 ASN F 174 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 HIS ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16806 Z= 0.284 Angle : 0.694 8.352 22665 Z= 0.368 Chirality : 0.044 0.317 2496 Planarity : 0.004 0.070 2911 Dihedral : 6.358 86.295 2220 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.72 % Favored : 91.70 % Rotamer: Outliers : 0.55 % Allowed : 7.60 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.18), residues: 2072 helix: 0.76 (0.19), residues: 761 sheet: -1.16 (0.29), residues: 331 loop : -1.92 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 131 HIS 0.008 0.001 HIS A 214 PHE 0.023 0.002 PHE F 257 TYR 0.016 0.002 TYR B 280 ARG 0.007 0.001 ARG G 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.3016 (tpt) cc_final: 0.2182 (tpt) REVERT: H 288 MET cc_start: 0.6852 (ppp) cc_final: 0.6449 (ppp) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 0.2563 time to fit residues: 41.8882 Evaluate side-chains 98 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 203 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 30.0000 chunk 126 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 186 optimal weight: 0.0370 chunk 201 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 HIS ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4805 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16806 Z= 0.155 Angle : 0.629 10.701 22665 Z= 0.330 Chirality : 0.043 0.342 2496 Planarity : 0.003 0.066 2911 Dihedral : 5.560 57.398 2216 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.90 % Favored : 92.62 % Rotamer: Outliers : 0.83 % Allowed : 9.31 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.96 (0.19), residues: 2072 helix: 1.03 (0.19), residues: 761 sheet: -1.10 (0.29), residues: 341 loop : -1.86 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 131 HIS 0.004 0.001 HIS B 231 PHE 0.017 0.001 PHE F 257 TYR 0.011 0.001 TYR B 280 ARG 0.004 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.2543 (tpt) cc_final: 0.1991 (tpt) REVERT: B 233 MET cc_start: 0.5168 (ppp) cc_final: 0.4158 (ppp) REVERT: E 255 MET cc_start: 0.7067 (mtp) cc_final: 0.6844 (mtp) REVERT: E 341 MET cc_start: 0.6296 (tmm) cc_final: 0.5643 (tmm) REVERT: G 117 MET cc_start: 0.6004 (ppp) cc_final: 0.5797 (ppp) REVERT: H 233 MET cc_start: -0.0290 (ppp) cc_final: -0.1077 (ppp) REVERT: H 288 MET cc_start: 0.7356 (ppp) cc_final: 0.6876 (ppp) outliers start: 15 outliers final: 3 residues processed: 107 average time/residue: 0.2491 time to fit residues: 43.1016 Evaluate side-chains 93 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 255 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 187 optimal weight: 0.3980 chunk 198 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 40 ASN A 345 HIS ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16806 Z= 0.316 Angle : 0.728 13.208 22665 Z= 0.378 Chirality : 0.043 0.213 2496 Planarity : 0.004 0.062 2911 Dihedral : 5.578 34.672 2216 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.59 % Favored : 90.97 % Rotamer: Outliers : 1.38 % Allowed : 11.35 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2072 helix: 0.61 (0.19), residues: 773 sheet: -1.08 (0.29), residues: 339 loop : -1.92 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 131 HIS 0.006 0.001 HIS F 214 PHE 0.026 0.002 PHE H 251 TYR 0.016 0.002 TYR F 123 ARG 0.006 0.001 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.2461 (tpt) cc_final: 0.1583 (tpt) REVERT: B 48 MET cc_start: 0.0702 (ppp) cc_final: 0.0473 (ppp) REVERT: B 233 MET cc_start: 0.5460 (ppp) cc_final: 0.4811 (ppp) REVERT: E 145 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.5453 (tp30) REVERT: E 255 MET cc_start: 0.7176 (mtp) cc_final: 0.6822 (mtp) REVERT: H 233 MET cc_start: -0.0304 (ppp) cc_final: -0.0738 (ppp) REVERT: H 288 MET cc_start: 0.7137 (ppp) cc_final: 0.6720 (ppp) outliers start: 25 outliers final: 11 residues processed: 112 average time/residue: 0.2695 time to fit residues: 47.9718 Evaluate side-chains 101 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 203 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 169 optimal weight: 30.0000 chunk 136 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 101 optimal weight: 0.0870 chunk 177 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4914 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16806 Z= 0.164 Angle : 0.650 11.485 22665 Z= 0.335 Chirality : 0.042 0.194 2496 Planarity : 0.004 0.103 2911 Dihedral : 5.103 32.101 2210 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.67 % Favored : 91.99 % Rotamer: Outliers : 1.05 % Allowed : 12.89 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.97 (0.19), residues: 2072 helix: 0.98 (0.19), residues: 768 sheet: -1.09 (0.29), residues: 339 loop : -1.86 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 22 HIS 0.005 0.001 HIS F 214 PHE 0.019 0.001 PHE F 257 TYR 0.009 0.001 TYR G 123 ARG 0.004 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.2582 (tpt) cc_final: 0.1769 (tpt) REVERT: B 233 MET cc_start: 0.4936 (ppp) cc_final: 0.4318 (ppp) REVERT: E 145 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5632 (tp30) REVERT: E 255 MET cc_start: 0.7043 (mtp) cc_final: 0.6718 (mtp) REVERT: E 341 MET cc_start: 0.6815 (tmm) cc_final: 0.6459 (tmm) REVERT: F 178 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6400 (mmm) REVERT: H 288 MET cc_start: 0.6972 (ppp) cc_final: 0.6630 (ppp) outliers start: 19 outliers final: 8 residues processed: 105 average time/residue: 0.2422 time to fit residues: 41.8155 Evaluate side-chains 96 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 255 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.0020 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 40.0000 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 164 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4974 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16806 Z= 0.198 Angle : 0.654 11.021 22665 Z= 0.336 Chirality : 0.042 0.288 2496 Planarity : 0.004 0.069 2911 Dihedral : 5.055 31.232 2210 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.92 % Favored : 91.70 % Rotamer: Outliers : 1.76 % Allowed : 13.66 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.93 (0.19), residues: 2072 helix: 1.06 (0.19), residues: 769 sheet: -1.24 (0.28), residues: 357 loop : -1.80 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 131 HIS 0.005 0.001 HIS F 214 PHE 0.020 0.001 PHE F 257 TYR 0.011 0.001 TYR F 123 ARG 0.003 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 2.140 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: B 35 MET cc_start: 0.3195 (tpt) cc_final: 0.2223 (tpt) REVERT: B 233 MET cc_start: 0.5095 (ppp) cc_final: 0.4827 (ppp) REVERT: E 145 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5530 (tp30) REVERT: E 255 MET cc_start: 0.7037 (mtp) cc_final: 0.6837 (mtp) REVERT: E 341 MET cc_start: 0.6778 (tmm) cc_final: 0.5819 (tmm) REVERT: F 178 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6409 (mmm) REVERT: H 288 MET cc_start: 0.6946 (ppp) cc_final: 0.6652 (ppp) outliers start: 32 outliers final: 12 residues processed: 115 average time/residue: 0.2444 time to fit residues: 45.6488 Evaluate side-chains 102 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 244 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 113 optimal weight: 0.0980 chunk 144 optimal weight: 0.0050 chunk 112 optimal weight: 6.9990 chunk 166 optimal weight: 50.0000 chunk 110 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 overall best weight: 3.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5132 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16806 Z= 0.327 Angle : 0.752 11.120 22665 Z= 0.391 Chirality : 0.044 0.169 2496 Planarity : 0.005 0.076 2911 Dihedral : 5.526 34.084 2210 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.98 % Favored : 90.54 % Rotamer: Outliers : 1.43 % Allowed : 14.88 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.19 (0.19), residues: 2072 helix: 0.69 (0.19), residues: 778 sheet: -1.31 (0.28), residues: 353 loop : -1.86 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 22 HIS 0.008 0.002 HIS F 214 PHE 0.038 0.002 PHE E 43 TYR 0.023 0.002 TYR F 123 ARG 0.007 0.001 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 145 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.5157 (tp30) REVERT: E 255 MET cc_start: 0.7442 (mtp) cc_final: 0.7179 (mtp) REVERT: E 341 MET cc_start: 0.6752 (tmm) cc_final: 0.6381 (tmm) REVERT: F 178 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6504 (mmm) REVERT: H 178 MET cc_start: 0.1272 (pmm) cc_final: 0.0881 (pmm) REVERT: H 288 MET cc_start: 0.7010 (ppp) cc_final: 0.6738 (ppp) outliers start: 26 outliers final: 18 residues processed: 107 average time/residue: 0.2524 time to fit residues: 43.6258 Evaluate side-chains 106 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 244 ASN Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 chunk 18 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5073 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16806 Z= 0.237 Angle : 0.707 15.867 22665 Z= 0.361 Chirality : 0.043 0.178 2496 Planarity : 0.004 0.071 2911 Dihedral : 5.347 33.694 2210 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.35 % Favored : 91.22 % Rotamer: Outliers : 1.49 % Allowed : 15.59 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.09 (0.19), residues: 2072 helix: 0.82 (0.19), residues: 779 sheet: -1.31 (0.29), residues: 340 loop : -1.82 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 22 HIS 0.006 0.001 HIS F 214 PHE 0.022 0.002 PHE F 257 TYR 0.016 0.001 TYR F 123 ARG 0.004 0.000 ARG F 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.3055 (tmm) cc_final: 0.2411 (tmm) REVERT: B 35 MET cc_start: 0.2530 (tpt) cc_final: 0.1900 (mmp) REVERT: B 69 LEU cc_start: -0.3198 (OUTLIER) cc_final: -0.3412 (tp) REVERT: E 145 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5355 (tp30) REVERT: E 175 THR cc_start: 0.3103 (OUTLIER) cc_final: 0.2852 (p) REVERT: E 255 MET cc_start: 0.7145 (mtp) cc_final: 0.6905 (mtp) REVERT: E 341 MET cc_start: 0.6739 (tmm) cc_final: 0.6389 (tmm) REVERT: F 178 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.6165 (tpt) REVERT: G 186 LEU cc_start: -0.2793 (OUTLIER) cc_final: -0.3008 (mp) REVERT: G 288 MET cc_start: 0.6214 (pmm) cc_final: 0.5798 (pmm) REVERT: H 288 MET cc_start: 0.6955 (ppp) cc_final: 0.6748 (ppp) outliers start: 27 outliers final: 17 residues processed: 107 average time/residue: 0.2410 time to fit residues: 42.4866 Evaluate side-chains 109 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 244 ASN Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 50.0000 chunk 174 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G 312 HIS ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5265 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16806 Z= 0.439 Angle : 0.871 12.417 22665 Z= 0.453 Chirality : 0.047 0.269 2496 Planarity : 0.005 0.074 2911 Dihedral : 6.086 36.195 2210 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.62 % Favored : 89.00 % Rotamer: Outliers : 1.27 % Allowed : 16.25 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.18), residues: 2072 helix: 0.12 (0.18), residues: 794 sheet: -1.53 (0.29), residues: 351 loop : -2.15 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 22 HIS 0.009 0.002 HIS F 214 PHE 0.027 0.003 PHE F 257 TYR 0.037 0.002 TYR F 123 ARG 0.007 0.001 ARG F 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 MET cc_start: 0.2384 (tpt) cc_final: 0.1007 (mmp) REVERT: B 69 LEU cc_start: -0.3105 (OUTLIER) cc_final: -0.3340 (tp) REVERT: E 255 MET cc_start: 0.7322 (mtp) cc_final: 0.7075 (mtp) REVERT: F 178 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6307 (tpt) REVERT: G 186 LEU cc_start: -0.2824 (OUTLIER) cc_final: -0.3033 (mp) REVERT: G 254 MET cc_start: -0.1191 (tpt) cc_final: -0.1434 (tpt) REVERT: G 288 MET cc_start: 0.6277 (pmm) cc_final: 0.5789 (pmm) REVERT: H 233 MET cc_start: 0.0383 (ppp) cc_final: -0.0064 (ppp) REVERT: H 288 MET cc_start: 0.7088 (ppp) cc_final: 0.6863 (ppp) outliers start: 23 outliers final: 17 residues processed: 107 average time/residue: 0.2495 time to fit residues: 43.6478 Evaluate side-chains 104 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 244 ASN Chi-restraints excluded: chain H residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 16 optimal weight: 0.0570 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 overall best weight: 1.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5072 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16806 Z= 0.192 Angle : 0.738 18.040 22665 Z= 0.376 Chirality : 0.044 0.191 2496 Planarity : 0.004 0.069 2911 Dihedral : 5.497 35.256 2210 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.74 % Favored : 90.83 % Rotamer: Outliers : 1.16 % Allowed : 16.53 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 2072 helix: 0.68 (0.19), residues: 781 sheet: -1.43 (0.29), residues: 336 loop : -1.85 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 36 HIS 0.006 0.001 HIS B 231 PHE 0.020 0.002 PHE F 257 TYR 0.015 0.001 TYR H 34 ARG 0.005 0.000 ARG F 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.3328 (tmm) cc_final: 0.2774 (tmm) REVERT: B 35 MET cc_start: 0.2191 (tpt) cc_final: 0.0881 (mmp) REVERT: E 175 THR cc_start: 0.3422 (OUTLIER) cc_final: 0.3117 (p) REVERT: E 255 MET cc_start: 0.7032 (mtp) cc_final: 0.6807 (mtp) REVERT: E 341 MET cc_start: 0.6471 (tmm) cc_final: 0.5831 (tmm) REVERT: F 178 MET cc_start: 0.6658 (mmp) cc_final: 0.6311 (tpt) REVERT: G 288 MET cc_start: 0.6305 (pmm) cc_final: 0.5875 (pmm) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.2444 time to fit residues: 41.6028 Evaluate side-chains 100 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 167 optimal weight: 50.0000 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 ASN G 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.070156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.042754 restraints weight = 159538.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.040800 restraints weight = 175586.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.040870 restraints weight = 163455.310| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16806 Z= 0.365 Angle : 0.826 15.739 22665 Z= 0.424 Chirality : 0.045 0.222 2496 Planarity : 0.004 0.070 2911 Dihedral : 5.866 36.845 2210 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.57 % Favored : 89.00 % Rotamer: Outliers : 1.16 % Allowed : 16.86 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.55 (0.19), residues: 2072 helix: 0.35 (0.18), residues: 791 sheet: -1.73 (0.28), residues: 357 loop : -1.94 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 36 HIS 0.009 0.002 HIS F 214 PHE 0.027 0.002 PHE B 257 TYR 0.032 0.002 TYR F 123 ARG 0.007 0.001 ARG F 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.04 seconds wall clock time: 53 minutes 2.14 seconds (3182.14 seconds total)