Starting phenix.real_space_refine on Sat Feb 17 02:58:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dws_27758/02_2024/8dws_27758.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dws_27758/02_2024/8dws_27758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dws_27758/02_2024/8dws_27758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dws_27758/02_2024/8dws_27758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dws_27758/02_2024/8dws_27758.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dws_27758/02_2024/8dws_27758.pdb" } resolution = 3.73 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= 0.049 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 156 5.16 5 C 10927 2.51 5 N 2874 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 351": "OE1" <-> "OE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17229 Number of models: 1 Model: "" Number of chains: 7 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: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} 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: {'PTRANS': 9, 'TRANS': 337} Chain: "G" Number of atoms: 2737 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 345, 2737 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 9, 'TRANS': 335} 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: 9.74, per 1000 atoms: 0.57 Number of scatterers: 17229 At special positions: 0 Unit cell: (73.929, 145.264, 313.874, 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 156 16.00 O 3272 8.00 N 2874 7.00 C 10927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS D 361 " distance=2.04 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.08 Conformation dependent library (CDL) restraints added in 3.3 seconds 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4198 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 23 sheets defined 47.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 138 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: 3.706A pdb=" N LEU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.029A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.907A pdb=" N SER A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.810A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 314 through 333 removed outlier: 6.322A pdb=" N SER A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.570A pdb=" N LYS A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.077A pdb=" N VAL A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.794A 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 215 through 222 Processing helix chain 'B' and resid 222 through 229 removed outlier: 3.575A pdb=" N MET B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.530A 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 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.750A pdb=" N TYR B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.512A 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 315 through 328 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.315A pdb=" N VAL B 343 " --> pdb=" O LYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.964A pdb=" N VAL B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.923A pdb=" N SER D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 314 through 328 Processing helix chain 'D' and resid 328 through 334 removed outlier: 3.543A pdb=" N VAL D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.619A pdb=" N LYS D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL D 343 " --> pdb=" O LYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 removed outlier: 4.109A pdb=" N GLN D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 removed outlier: 4.124A pdb=" N CYS E 44 " --> pdb=" O PHE E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 removed outlier: 3.825A pdb=" N LEU E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 148 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.543A pdb=" N ASP E 153 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.846A pdb=" N HIS E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 259 removed outlier: 4.670A pdb=" N GLU E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 4.113A 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: 3.560A pdb=" N VAL E 332 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 328 through 333' Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.808A pdb=" N LYS E 339 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 359 removed outlier: 3.669A pdb=" N VAL E 349 " --> pdb=" O HIS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.865A pdb=" N ASP F 63 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 81 removed outlier: 3.843A pdb=" N LYS F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 81' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 145 through 148 Processing helix chain 'F' and resid 150 through 154 removed outlier: 3.518A pdb=" N ASP F 153 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 197 removed outlier: 3.958A pdb=" N LEU F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 222 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.534A pdb=" N MET F 228 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS F 231 " --> pdb=" O ALA F 227 " (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 265 through 268 removed outlier: 3.752A pdb=" N LYS F 268 " --> pdb=" O ASN F 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 284 through 295 removed outlier: 3.523A 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 314 through 328 Processing helix chain 'F' and resid 328 through 333 Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.548A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 356 removed outlier: 3.613A pdb=" N VAL F 349 " --> pdb=" O HIS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 138 through 144 Processing helix chain 'G' and resid 145 through 148 Processing helix chain 'G' and resid 150 through 154 removed outlier: 3.609A pdb=" N ASP G 153 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 197 removed outlier: 4.006A pdb=" N LEU G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 222 removed outlier: 3.846A pdb=" N LEU G 218 " --> pdb=" O HIS G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 230 removed outlier: 3.582A pdb=" N MET G 228 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 240 removed outlier: 3.807A pdb=" N ASN G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 260 Processing helix chain 'G' and resid 265 through 268 Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 282 through 295 removed outlier: 3.624A 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: 6.230A pdb=" N SER G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP G 331 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 removed outlier: 4.178A pdb=" N LYS G 339 " --> pdb=" O THR G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.900A pdb=" N VAL G 349 " --> pdb=" O HIS G 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 44 removed outlier: 3.579A pdb=" N PHE H 43 " --> pdb=" O ASN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 144 Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 150 through 154 Processing helix chain 'H' and resid 185 through 192 removed outlier: 3.644A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 3.709A pdb=" N ASN H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 222 removed outlier: 4.230A pdb=" N LEU H 218 " --> pdb=" O HIS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.678A pdb=" N GLU H 230 " --> pdb=" O SER H 226 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS H 231 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 261 removed outlier: 3.927A 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 removed outlier: 3.609A pdb=" N LEU H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.504A 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: 3.911A 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 358 removed outlier: 4.153A pdb=" N VAL H 349 " --> pdb=" O HIS H 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.660A pdb=" N ILE A 38 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 155 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A 156 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 101 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 104 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 117 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 72 removed outlier: 6.631A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 213 removed outlier: 8.804A pdb=" N ILE A 243 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N CYS A 205 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.647A pdb=" N ILE B 137 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 86 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS B 135 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 213 removed outlier: 3.878A pdb=" N VAL B 241 " --> pdb=" O CYS B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 23 through 25 removed outlier: 6.489A pdb=" N CYS E 23 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 155 " --> pdb=" O ILE G 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 115 through 118 Processing sheet with id=AB1, first strand: chain 'E' and resid 115 through 118 removed outlier: 3.846A pdb=" N LYS E 101 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N CYS F 23 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET E 35 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 66 through 72 removed outlier: 7.132A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS E 68 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N AARG E 70 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER E 85 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 211 through 213 removed outlier: 6.350A pdb=" N CYS E 203 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 28 through 29 removed outlier: 4.024A pdb=" N LYS F 28 " --> pdb=" O GLN F 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN F 165 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 164 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG F 99 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 57 through 59 removed outlier: 4.162A pdb=" N SER F 59 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU F 65 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS F 66 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 91 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N AARG F 70 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE F 137 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU F 86 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LYS F 135 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU F 88 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE F 133 " --> pdb=" O LEU F 88 " (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 28 through 33 removed outlier: 4.372A pdb=" N LYS G 28 " --> pdb=" O GLN G 165 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG G 99 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 100 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 123 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.562A pdb=" N VAL G 71 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS G 66 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 89 " --> pdb=" O CYS G 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N AARG G 70 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 85 " --> pdb=" O ASN G 72 " (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 removed outlier: 4.713A pdb=" N PHE H 158 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER H 105 " --> pdb=" O PHE H 158 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE H 102 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLU H 118 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE H 104 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA H 116 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE H 106 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 66 through 72 removed outlier: 7.277A pdb=" N LYS H 66 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN H 72 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER H 85 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 86 " --> pdb=" O PHE H 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AC5, first strand: chain 'H' and resid 205 through 206 697 hydrogen bonds defined for protein. 1926 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: 6.02 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5578 1.34 - 1.46: 3961 1.46 - 1.59: 7797 1.59 - 1.71: 0 1.71 - 1.83: 231 Bond restraints: 17567 Sorted by residual: bond pdb=" N SER G 171 " pdb=" CA SER G 171 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.06e+01 bond pdb=" N GLN G 173 " pdb=" CA GLN G 173 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" N ILE G 170 " pdb=" CA ILE G 170 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.35e-02 5.49e+03 9.09e+00 bond pdb=" N GLU E 46 " pdb=" CA GLU E 46 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.36e+00 bond pdb=" N ASP G 166 " pdb=" CA ASP G 166 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.25e-02 6.40e+03 7.90e+00 ... (remaining 17562 not shown) Histogram of bond angle deviations from ideal: 99.25 - 107.80: 619 107.80 - 116.35: 11121 116.35 - 124.89: 11595 124.89 - 133.44: 319 133.44 - 141.99: 38 Bond angle restraints: 23692 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 121.54 141.99 -20.45 1.91e+00 2.74e-01 1.15e+02 angle pdb=" C ASP G 166 " pdb=" CA ASP G 166 " pdb=" CB ASP G 166 " ideal model delta sigma weight residual 109.64 118.86 -9.22 1.77e+00 3.19e-01 2.71e+01 angle pdb=" CA ILE G 170 " pdb=" C ILE G 170 " pdb=" O ILE G 170 " ideal model delta sigma weight residual 121.98 116.42 5.56 1.21e+00 6.83e-01 2.11e+01 angle pdb=" C VAL D 342 " pdb=" N VAL D 343 " pdb=" CA VAL D 343 " ideal model delta sigma weight residual 121.97 130.03 -8.06 1.80e+00 3.09e-01 2.00e+01 angle pdb=" C VAL B 168 " pdb=" N ASN B 169 " pdb=" CA ASN B 169 " ideal model delta sigma weight residual 121.70 129.48 -7.78 1.80e+00 3.09e-01 1.87e+01 ... (remaining 23687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9678 17.97 - 35.94: 834 35.94 - 53.91: 139 53.91 - 71.88: 30 71.88 - 89.85: 18 Dihedral angle restraints: 10699 sinusoidal: 4269 harmonic: 6430 Sorted by residual: 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 -180.00 -126.53 -53.47 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA SER G 167 " pdb=" C SER G 167 " pdb=" N VAL G 168 " pdb=" CA VAL G 168 " ideal model delta harmonic sigma weight residual 180.00 138.67 41.33 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA GLN H 360 " pdb=" C GLN H 360 " pdb=" N CYS H 361 " pdb=" CA CYS H 361 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 10696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2498 0.099 - 0.199: 113 0.199 - 0.298: 4 0.298 - 0.397: 2 0.397 - 0.497: 2 Chirality restraints: 2619 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 2.01 0.50 2.00e-01 2.50e+01 6.17e+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 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA LYS E 47 " pdb=" N LYS E 47 " pdb=" C LYS E 47 " pdb=" CB LYS E 47 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 2616 not shown) Planarity restraints: 3037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 43 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C PHE E 43 " 0.070 2.00e-02 2.50e+03 pdb=" O PHE E 43 " -0.027 2.00e-02 2.50e+03 pdb=" N CYS E 44 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 52 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C ILE E 52 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE E 52 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS E 53 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 169 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C ASN G 169 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN G 169 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE G 170 " 0.016 2.00e-02 2.50e+03 ... (remaining 3034 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 164 2.59 - 3.17: 15273 3.17 - 3.75: 26430 3.75 - 4.32: 34497 4.32 - 4.90: 57045 Nonbonded interactions: 133409 Sorted by model distance: nonbonded pdb=" OG SER G 21 " pdb=" O MET H 35 " model vdw 2.013 2.440 nonbonded pdb=" OG1 THR G 25 " pdb=" O THR H 37 " model vdw 2.061 2.440 nonbonded pdb=" OG SER F 54 " pdb=" O LEU F 69 " model vdw 2.063 2.440 nonbonded pdb=" O LEU E 76 " pdb=" OG SER E 80 " model vdw 2.084 2.440 nonbonded pdb=" O VAL D 332 " pdb=" OG1 THR D 335 " model vdw 2.091 2.440 ... (remaining 133404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.530 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 49.470 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4530 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 0.052 17567 Z= 0.284 Angle : 0.788 20.445 23692 Z= 0.433 Chirality : 0.047 0.497 2619 Planarity : 0.004 0.065 3037 Dihedral : 14.369 89.853 6495 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.16 % Favored : 91.24 % Rotamer: Outliers : 0.32 % Allowed : 0.47 % Favored : 99.21 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.47 (0.18), residues: 2168 helix: 0.34 (0.18), residues: 826 sheet: -1.48 (0.28), residues: 345 loop : -1.92 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 67 HIS 0.005 0.001 HIS E 347 PHE 0.029 0.002 PHE E 136 TYR 0.026 0.002 TYR A 259 ARG 0.005 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 254 MET cc_start: 0.7340 (ttp) cc_final: 0.7110 (ttm) REVERT: G 353 TYR cc_start: 0.0306 (t80) cc_final: -0.1649 (m-80) REVERT: H 178 MET cc_start: 0.2555 (pmm) cc_final: 0.2133 (pmm) outliers start: 6 outliers final: 1 residues processed: 130 average time/residue: 0.2951 time to fit residues: 59.5754 Evaluate side-chains 98 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 ASN E 326 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G 212 GLN ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4646 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17567 Z= 0.228 Angle : 0.639 8.482 23692 Z= 0.338 Chirality : 0.042 0.167 2619 Planarity : 0.004 0.057 3037 Dihedral : 5.411 55.649 2316 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.43 % Favored : 91.97 % Rotamer: Outliers : 0.47 % Allowed : 6.43 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2168 helix: 0.81 (0.18), residues: 852 sheet: -1.42 (0.29), residues: 317 loop : -1.86 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 22 HIS 0.004 0.001 HIS D 312 PHE 0.018 0.001 PHE F 257 TYR 0.035 0.002 TYR H 24 ARG 0.004 0.000 AARG G 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.954 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 228 MET cc_start: 0.4168 (ptm) cc_final: 0.3763 (ptm) REVERT: E 63 ASP cc_start: 0.4932 (OUTLIER) cc_final: 0.4709 (m-30) REVERT: G 353 TYR cc_start: 0.0452 (t80) cc_final: -0.1414 (m-80) outliers start: 9 outliers final: 3 residues processed: 107 average time/residue: 0.2863 time to fit residues: 48.2906 Evaluate side-chains 100 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain G residue 175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 HIS ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4851 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17567 Z= 0.361 Angle : 0.733 11.365 23692 Z= 0.386 Chirality : 0.043 0.188 2619 Planarity : 0.004 0.048 3037 Dihedral : 5.615 43.126 2316 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.76 % Favored : 90.73 % Rotamer: Outliers : 1.05 % Allowed : 10.60 % Favored : 88.34 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -1.13 (0.18), residues: 2168 helix: 0.77 (0.18), residues: 848 sheet: -1.30 (0.29), residues: 321 loop : -1.93 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 36 HIS 0.007 0.001 HIS H 214 PHE 0.025 0.002 PHE F 257 TYR 0.027 0.002 TYR H 83 ARG 0.005 0.001 AARG B 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 353 TYR cc_start: 0.0126 (t80) cc_final: -0.1414 (m-80) outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 0.2709 time to fit residues: 48.1900 Evaluate side-chains 102 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 185 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN D 328 HIS ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4745 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17567 Z= 0.182 Angle : 0.604 10.557 23692 Z= 0.317 Chirality : 0.041 0.266 2619 Planarity : 0.003 0.058 3037 Dihedral : 5.254 49.808 2316 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.80 % Favored : 91.70 % Rotamer: Outliers : 1.16 % Allowed : 13.13 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 2168 helix: 1.12 (0.18), residues: 855 sheet: -1.35 (0.30), residues: 322 loop : -1.79 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 36 HIS 0.005 0.001 HIS H 214 PHE 0.019 0.001 PHE F 257 TYR 0.017 0.001 TYR F 83 ARG 0.003 0.000 AARG B 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 331 ASP cc_start: 0.5140 (t0) cc_final: 0.4940 (t0) REVERT: G 353 TYR cc_start: 0.1110 (t80) cc_final: -0.0889 (m-80) outliers start: 22 outliers final: 11 residues processed: 111 average time/residue: 0.2760 time to fit residues: 48.9448 Evaluate side-chains 105 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 361 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 GLN ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4866 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17567 Z= 0.310 Angle : 0.678 10.736 23692 Z= 0.354 Chirality : 0.042 0.243 2619 Planarity : 0.004 0.048 3037 Dihedral : 5.416 43.611 2316 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.13 % Favored : 90.31 % Rotamer: Outliers : 2.11 % Allowed : 14.03 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: 2168 helix: 0.98 (0.18), residues: 862 sheet: -1.33 (0.28), residues: 351 loop : -1.91 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 36 HIS 0.013 0.001 HIS D 328 PHE 0.025 0.002 PHE F 257 TYR 0.043 0.002 TYR F 83 ARG 0.005 0.001 ARG H 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 93 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.6683 (tmm) cc_final: 0.5936 (mpp) REVERT: F 178 MET cc_start: 0.5882 (mmm) cc_final: 0.5679 (mmm) REVERT: G 353 TYR cc_start: 0.0175 (t80) cc_final: -0.1358 (m-80) outliers start: 40 outliers final: 24 residues processed: 125 average time/residue: 0.2648 time to fit residues: 53.2708 Evaluate side-chains 115 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 361 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 207 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4776 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17567 Z= 0.178 Angle : 0.619 11.039 23692 Z= 0.323 Chirality : 0.041 0.241 2619 Planarity : 0.003 0.053 3037 Dihedral : 5.214 48.710 2316 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.16 % Favored : 91.33 % Rotamer: Outliers : 1.42 % Allowed : 15.61 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 2168 helix: 1.22 (0.18), residues: 866 sheet: -1.26 (0.29), residues: 340 loop : -1.92 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 194 HIS 0.008 0.001 HIS D 347 PHE 0.018 0.001 PHE F 257 TYR 0.035 0.001 TYR F 83 ARG 0.003 0.000 ARG E 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.6815 (tmm) cc_final: 0.6080 (mpp) REVERT: G 353 TYR cc_start: 0.1156 (t80) cc_final: -0.0484 (m-80) REVERT: H 254 MET cc_start: 0.7265 (ppp) cc_final: 0.6903 (ppp) REVERT: H 341 MET cc_start: 0.4936 (tmm) cc_final: 0.4608 (tmm) outliers start: 27 outliers final: 16 residues processed: 117 average time/residue: 0.2661 time to fit residues: 50.4238 Evaluate side-chains 108 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 361 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 174 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4852 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17567 Z= 0.250 Angle : 0.666 10.742 23692 Z= 0.345 Chirality : 0.042 0.270 2619 Planarity : 0.003 0.046 3037 Dihedral : 5.224 44.372 2316 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.04 % Favored : 90.50 % Rotamer: Outliers : 1.64 % Allowed : 16.14 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.82 (0.19), residues: 2168 helix: 1.18 (0.18), residues: 863 sheet: -1.32 (0.28), residues: 362 loop : -1.89 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 36 HIS 0.009 0.001 HIS D 347 PHE 0.022 0.001 PHE F 257 TYR 0.019 0.002 TYR A 83 ARG 0.004 0.000 ARG H 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 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 176 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6013 (mpp) REVERT: G 115 LYS cc_start: 0.0777 (OUTLIER) cc_final: -0.0060 (pttm) REVERT: G 353 TYR cc_start: 0.1155 (t80) cc_final: -0.0450 (m-80) REVERT: H 176 MET cc_start: 0.2481 (tmm) cc_final: 0.1367 (mmp) REVERT: H 233 MET cc_start: 0.1470 (ppp) cc_final: 0.0645 (ptm) REVERT: H 341 MET cc_start: 0.5088 (tmm) cc_final: 0.4792 (tmm) outliers start: 31 outliers final: 21 residues processed: 117 average time/residue: 0.2697 time to fit residues: 50.7868 Evaluate side-chains 114 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 115 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 0.0670 chunk 19 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 overall best weight: 2.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4830 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17567 Z= 0.214 Angle : 0.665 14.173 23692 Z= 0.339 Chirality : 0.042 0.292 2619 Planarity : 0.003 0.050 3037 Dihedral : 5.157 46.073 2316 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.58 % Favored : 91.01 % Rotamer: Outliers : 1.79 % Allowed : 16.46 % Favored : 81.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 2168 helix: 1.24 (0.18), residues: 865 sheet: -1.29 (0.28), residues: 366 loop : -1.93 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 36 HIS 0.010 0.001 HIS D 347 PHE 0.020 0.001 PHE F 257 TYR 0.016 0.001 TYR A 83 ARG 0.004 0.000 ARG H 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 115 LYS cc_start: 0.1053 (OUTLIER) cc_final: 0.0249 (pttm) REVERT: G 353 TYR cc_start: 0.0836 (t80) cc_final: -0.0704 (m-80) REVERT: H 176 MET cc_start: 0.2732 (tmm) cc_final: 0.1405 (mmp) REVERT: H 341 MET cc_start: 0.5193 (tmm) cc_final: 0.4900 (tmm) outliers start: 34 outliers final: 26 residues processed: 117 average time/residue: 0.2649 time to fit residues: 50.0161 Evaluate side-chains 115 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain D residue 347 HIS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 115 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.4980 chunk 180 optimal weight: 10.0000 chunk 192 optimal weight: 0.2980 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 173 optimal weight: 30.0000 chunk 181 optimal weight: 0.6980 chunk 191 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4892 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17567 Z= 0.270 Angle : 0.709 12.333 23692 Z= 0.360 Chirality : 0.042 0.297 2619 Planarity : 0.004 0.046 3037 Dihedral : 5.326 42.731 2316 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.95 % Favored : 90.59 % Rotamer: Outliers : 1.79 % Allowed : 16.67 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -0.86 (0.19), residues: 2168 helix: 1.14 (0.18), residues: 859 sheet: -1.22 (0.28), residues: 365 loop : -1.96 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 36 HIS 0.008 0.001 HIS D 347 PHE 0.024 0.002 PHE F 257 TYR 0.015 0.002 TYR E 280 ARG 0.005 0.001 ARG H 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.6612 (tmm) cc_final: 0.6141 (mpp) REVERT: G 115 LYS cc_start: 0.1073 (OUTLIER) cc_final: 0.0244 (pttm) REVERT: G 353 TYR cc_start: 0.0541 (t80) cc_final: -0.0574 (m-80) REVERT: H 176 MET cc_start: 0.2173 (tmm) cc_final: 0.1066 (mmp) outliers start: 34 outliers final: 29 residues processed: 118 average time/residue: 0.3302 time to fit residues: 61.7760 Evaluate side-chains 118 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** H 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4866 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17567 Z= 0.230 Angle : 0.690 12.195 23692 Z= 0.350 Chirality : 0.042 0.297 2619 Planarity : 0.003 0.048 3037 Dihedral : 5.264 45.864 2316 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.44 % Favored : 91.10 % Rotamer: Outliers : 1.85 % Allowed : 16.67 % Favored : 81.49 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 2168 helix: 1.13 (0.18), residues: 862 sheet: -1.25 (0.28), residues: 368 loop : -1.87 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 36 HIS 0.007 0.001 HIS H 214 PHE 0.021 0.001 PHE F 257 TYR 0.015 0.001 TYR E 280 ARG 0.004 0.000 ARG H 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 91 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.6435 (tmm) cc_final: 0.6078 (mpp) REVERT: G 115 LYS cc_start: 0.1315 (OUTLIER) cc_final: 0.0523 (pttm) REVERT: G 353 TYR cc_start: 0.0551 (t80) cc_final: -0.0584 (m-80) REVERT: H 176 MET cc_start: 0.2671 (tmm) cc_final: 0.1206 (mmp) REVERT: H 341 MET cc_start: 0.5292 (tmm) cc_final: 0.5051 (tmm) outliers start: 35 outliers final: 28 residues processed: 122 average time/residue: 0.2879 time to fit residues: 54.8891 Evaluate side-chains 120 residues out of total 1899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain H residue 241 VAL Chi-restraints excluded: chain H residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 71 optimal weight: 50.0000 chunk 174 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 149 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN ** H 347 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 = 0.4257 r_free = 0.4257 target = 0.076205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.043254 restraints weight = 170207.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.043344 restraints weight = 109104.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.042400 restraints weight = 85622.472| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17567 Z= 0.425 Angle : 0.844 11.216 23692 Z= 0.435 Chirality : 0.045 0.314 2619 Planarity : 0.005 0.051 3037 Dihedral : 5.868 38.456 2316 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.56 % Favored : 88.88 % Rotamer: Outliers : 1.85 % Allowed : 16.88 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.14 % 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: -1.42 (0.18), residues: 2168 helix: 0.45 (0.18), residues: 862 sheet: -1.34 (0.29), residues: 351 loop : -2.11 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 36 HIS 0.022 0.002 HIS D 328 PHE 0.031 0.002 PHE F 257 TYR 0.022 0.003 TYR H 87 ARG 0.008 0.001 ARG E 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3448.89 seconds wall clock time: 65 minutes 13.14 seconds (3913.14 seconds total)