Starting phenix.real_space_refine on Fri Feb 16 20:28:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wum_21916/02_2024/6wum_21916.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wum_21916/02_2024/6wum_21916.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/6wum_21916/02_2024/6wum_21916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wum_21916/02_2024/6wum_21916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wum_21916/02_2024/6wum_21916.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wum_21916/02_2024/6wum_21916.pdb" } 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= 0.024 sd= 0.131 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 30 5.16 5 C 10420 2.51 5 N 2924 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 60": "OD1" <-> "OD2" Residue "E ASP 85": "OD1" <-> "OD2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE -25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 18": "OD1" <-> "OD2" Residue "b TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 243": "OE1" <-> "OE2" Residue "b GLU 248": "OE1" <-> "OE2" Residue "b GLU 255": "OE1" <-> "OE2" Residue "b TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 326": "OD1" <-> "OD2" Residue "b PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 386": "OD1" <-> "OD2" Residue "b PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 71": "OE1" <-> "OE2" Residue "a ASP 72": "OD1" <-> "OD2" Residue "a ASP 98": "OD1" <-> "OD2" Residue "a PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 102": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a ASP 145": "OD1" <-> "OD2" Residue "a PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 436": "OD1" <-> "OD2" Residue "a ARG 482": "NH1" <-> "NH2" Residue "a GLU 484": "OE1" <-> "OE2" Residue "a ARG 494": "NH1" <-> "NH2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE -25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ARG 494": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16414 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2284 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 22, 'TRANS': 272} Chain breaks: 2 Chain: "b" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2614 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 3 Chain: "a" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3309 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2284 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 22, 'TRANS': 272} Chain breaks: 2 Chain: "C" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2614 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 3 Chain: "B" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3309 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Time building chain proxies: 9.35, per 1000 atoms: 0.57 Number of scatterers: 16414 At special positions: 0 Unit cell: (156.88, 121.9, 115.54, 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 30 16.00 O 3040 8.00 N 2924 7.00 C 10420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.8 seconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 26 sheets defined 37.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.782A pdb=" N ARG E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 82 removed outlier: 4.662A pdb=" N TRP E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 Processing helix chain 'E' and resid 150 through 174 removed outlier: 3.840A pdb=" N ALA E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 160 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG E 165 " --> pdb=" O THR E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 178 through 187 Processing helix chain 'E' and resid 193 through 213 removed outlier: 4.135A pdb=" N ALA E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN E 211 " --> pdb=" O ALA E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 255 removed outlier: 3.762A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.907A pdb=" N TYR E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 285 Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 300 through 307 removed outlier: 3.699A pdb=" N MET E 304 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'b' and resid 18 through 32 removed outlier: 3.766A pdb=" N LEU b 22 " --> pdb=" O ASP b 18 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 47 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 106 through 121 Processing helix chain 'b' and resid 125 through 130 removed outlier: 3.731A pdb=" N LEU b 129 " --> pdb=" O PRO b 125 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 148 Processing helix chain 'b' and resid 153 through 156 removed outlier: 3.830A pdb=" N TRP b 156 " --> pdb=" O PRO b 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 153 through 156' Processing helix chain 'b' and resid 157 through 171 removed outlier: 3.593A pdb=" N ALA b 161 " --> pdb=" O THR b 157 " (cutoff:3.500A) Processing helix chain 'b' and resid 239 through 254 removed outlier: 3.674A pdb=" N VAL b 249 " --> pdb=" O ALA b 245 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL b 252 " --> pdb=" O GLU b 248 " (cutoff:3.500A) Processing helix chain 'b' and resid 255 through 257 No H-bonds generated for 'chain 'b' and resid 255 through 257' Processing helix chain 'b' and resid 268 through 284 removed outlier: 3.715A pdb=" N LEU b 274 " --> pdb=" O GLU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 291 through 299 removed outlier: 3.545A pdb=" N ILE b 295 " --> pdb=" O TRP b 291 " (cutoff:3.500A) Processing helix chain 'b' and resid 300 through 315 removed outlier: 3.765A pdb=" N CYS b 304 " --> pdb=" O TYR b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 319 Processing helix chain 'b' and resid 328 through 333 removed outlier: 4.432A pdb=" N ALA b 333 " --> pdb=" O ALA b 329 " (cutoff:3.500A) Processing helix chain 'b' and resid 338 through 352 Processing helix chain 'b' and resid 356 through 378 removed outlier: 4.738A pdb=" N TRP b 360 " --> pdb=" O LEU b 356 " (cutoff:3.500A) Processing helix chain 'b' and resid 386 through 407 removed outlier: 3.696A pdb=" N TYR b 407 " --> pdb=" O GLY b 403 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 70 removed outlier: 3.664A pdb=" N LEU a 62 " --> pdb=" O ARG a 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE a 65 " --> pdb=" O LEU a 61 " (cutoff:3.500A) Proline residue: a 68 - end of helix Processing helix chain 'a' and resid 86 through 96 Processing helix chain 'a' and resid 211 through 214 removed outlier: 3.704A pdb=" N SER a 214 " --> pdb=" O PRO a 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 211 through 214' Processing helix chain 'a' and resid 257 through 261 Processing helix chain 'a' and resid 447 through 462 removed outlier: 3.540A pdb=" N THR a 462 " --> pdb=" O VAL a 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.782A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.663A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.841A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.135A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.762A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.907A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 307 removed outlier: 3.699A pdb=" N MET A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'C' and resid 18 through 32 removed outlier: 3.767A pdb=" N LEU C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.731A pdb=" N LEU C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.831A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 171 removed outlier: 3.594A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.674A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.714A pdb=" N LEU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.546A pdb=" N ILE C 295 " --> pdb=" O TRP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.766A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 328 through 333 removed outlier: 4.432A pdb=" N ALA C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 356 through 378 removed outlier: 4.738A pdb=" N TRP C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 407 removed outlier: 3.695A pdb=" N TYR C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.664A pdb=" N LEU B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 86 through 96 Processing helix chain 'B' and resid 211 through 214 removed outlier: 3.704A pdb=" N SER B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.539A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 30 through 31 removed outlier: 5.668A pdb=" N ARG E 30 " --> pdb=" O LEU a 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.484A pdb=" N LEU E 52 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'b' and resid 419 through 421 removed outlier: 5.861A pdb=" N THR a 48 " --> pdb=" O ILE a 128 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE a 130 " --> pdb=" O THR a 48 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU a 50 " --> pdb=" O ILE a 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 139 through 142 removed outlier: 4.324A pdb=" N TYR a 183 " --> pdb=" O ARG a 205 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG a 205 " --> pdb=" O TYR a 183 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER a 242 " --> pdb=" O ALA a 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE a 291 " --> pdb=" O ARG a 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 198 through 210 removed outlier: 3.689A pdb=" N GLU a 217 " --> pdb=" O THR a 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 290 through 297 Processing sheet with id=AA8, first strand: chain 'a' and resid 311 through 316 removed outlier: 4.135A pdb=" N LEU a 339 " --> pdb=" O ALA a 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 319 through 320 Processing sheet with id=AB1, first strand: chain 'a' and resid 356 through 357 Processing sheet with id=AB2, first strand: chain 'a' and resid 396 through 397 removed outlier: 3.863A pdb=" N ARG a 426 " --> pdb=" O ALA a 397 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 400 through 401 removed outlier: 4.053A pdb=" N VAL a 401 " --> pdb=" O ALA a 422 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 405 through 406 Processing sheet with id=AB5, first strand: chain 'A' and resid 30 through 31 removed outlier: 5.703A pdb=" N ARG A 30 " --> pdb=" O LEU B 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.484A pdb=" N LEU A 52 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB8, first strand: chain 'C' and resid 417 through 421 removed outlier: 3.774A pdb=" N GLN C 418 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR B 48 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 130 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU B 50 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 139 through 142 removed outlier: 4.324A pdb=" N TYR B 183 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 205 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 242 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 291 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 198 through 210 removed outlier: 3.689A pdb=" N GLU B 217 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 290 through 297 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 316 removed outlier: 4.136A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AC6, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.864A pdb=" N ARG B 426 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 400 through 401 removed outlier: 4.054A pdb=" N VAL B 401 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 405 through 406 631 hydrogen bonds defined for protein. 1761 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: 4.57 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3799 1.33 - 1.45: 3522 1.45 - 1.57: 9421 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 16792 Sorted by residual: bond pdb=" C ASP A 148 " pdb=" N LEU A 149 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.48e-02 4.57e+03 4.43e+00 bond pdb=" C SER A 257 " pdb=" N GLU A 258 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.41e-02 5.03e+03 4.27e+00 bond pdb=" C ASP E 148 " pdb=" N LEU E 149 " ideal model delta sigma weight residual 1.331 1.300 0.030 1.48e-02 4.57e+03 4.24e+00 bond pdb=" C SER E 257 " pdb=" N GLU E 258 " ideal model delta sigma weight residual 1.332 1.305 0.028 1.41e-02 5.03e+03 3.87e+00 bond pdb=" C ALA C 2 " pdb=" N VAL C 3 " ideal model delta sigma weight residual 1.335 1.312 0.023 1.27e-02 6.20e+03 3.33e+00 ... (remaining 16787 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.26: 574 106.26 - 113.21: 9143 113.21 - 120.16: 6247 120.16 - 127.11: 6621 127.11 - 134.06: 263 Bond angle restraints: 22848 Sorted by residual: angle pdb=" N LEU b 284 " pdb=" CA LEU b 284 " pdb=" C LEU b 284 " ideal model delta sigma weight residual 109.81 118.31 -8.50 2.21e+00 2.05e-01 1.48e+01 angle pdb=" N LEU C 284 " pdb=" CA LEU C 284 " pdb=" C LEU C 284 " ideal model delta sigma weight residual 109.81 118.29 -8.48 2.21e+00 2.05e-01 1.47e+01 angle pdb=" N ASN E 35 " pdb=" CA ASN E 35 " pdb=" C ASN E 35 " ideal model delta sigma weight residual 110.68 115.95 -5.27 1.39e+00 5.18e-01 1.44e+01 angle pdb=" N ASN A 35 " pdb=" CA ASN A 35 " pdb=" C ASN A 35 " ideal model delta sigma weight residual 110.68 115.92 -5.24 1.39e+00 5.18e-01 1.42e+01 angle pdb=" N ALA b 11 " pdb=" CA ALA b 11 " pdb=" C ALA b 11 " ideal model delta sigma weight residual 110.80 118.32 -7.52 2.13e+00 2.20e-01 1.25e+01 ... (remaining 22843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9060 17.97 - 35.93: 769 35.93 - 53.90: 105 53.90 - 71.87: 20 71.87 - 89.83: 18 Dihedral angle restraints: 9972 sinusoidal: 3814 harmonic: 6158 Sorted by residual: dihedral pdb=" CA LEU E 101 " pdb=" C LEU E 101 " pdb=" N PRO E 102 " pdb=" CA PRO E 102 " ideal model delta harmonic sigma weight residual -180.00 -144.60 -35.40 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta harmonic sigma weight residual -180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA TYR B 183 " pdb=" C TYR B 183 " pdb=" N ASN B 184 " pdb=" CA ASN B 184 " ideal model delta harmonic sigma weight residual 180.00 148.27 31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 9969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2238 0.074 - 0.148: 321 0.148 - 0.222: 11 0.222 - 0.295: 0 0.295 - 0.369: 2 Chirality restraints: 2572 Sorted by residual: chirality pdb=" CA GLU A 258 " pdb=" N GLU A 258 " pdb=" C GLU A 258 " pdb=" CB GLU A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA GLU E 258 " pdb=" N GLU E 258 " pdb=" C GLU E 258 " pdb=" CB GLU E 258 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA LEU b 52 " pdb=" N LEU b 52 " pdb=" C LEU b 52 " pdb=" CB LEU b 52 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2569 not shown) Planarity restraints: 2966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 258 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C GLU E 258 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU E 258 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 259 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 257 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C SER A 257 " 0.033 2.00e-02 2.50e+03 pdb=" O SER A 257 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 258 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 383 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO B 384 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " 0.026 5.00e-02 4.00e+02 ... (remaining 2963 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 417 2.65 - 3.21: 15778 3.21 - 3.77: 23641 3.77 - 4.34: 32222 4.34 - 4.90: 54112 Nonbonded interactions: 126170 Sorted by model distance: nonbonded pdb=" O HIS b 51 " pdb=" OG1 THR b 54 " model vdw 2.086 2.440 nonbonded pdb=" O HIS C 51 " pdb=" OG1 THR C 54 " model vdw 2.087 2.440 nonbonded pdb=" OG SER A 96 " pdb=" O THR A 98 " model vdw 2.159 2.440 nonbonded pdb=" OG SER E 96 " pdb=" O THR E 98 " model vdw 2.160 2.440 nonbonded pdb=" NE1 TRP b 420 " pdb=" OD1 ASP a 63 " model vdw 2.169 2.520 ... (remaining 126165 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'a' } ncs_group { reference = chain 'C' selection = chain 'b' } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.750 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 42.360 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.008 0.074 16792 Z= 0.531 Angle : 0.923 8.499 22848 Z= 0.527 Chirality : 0.050 0.369 2572 Planarity : 0.005 0.047 2966 Dihedral : 13.760 89.834 6020 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.45 % Favored : 83.46 % Rotamer: Outliers : 1.01 % Allowed : 7.35 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.30 % 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: -4.27 (0.16), residues: 2128 helix: -1.31 (0.17), residues: 740 sheet: -3.68 (0.21), residues: 442 loop : -3.64 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 361 HIS 0.007 0.002 HIS B 215 PHE 0.028 0.002 PHE a 396 TYR 0.027 0.002 TYR b 37 ARG 0.004 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 248 ASP cc_start: 0.7418 (t0) cc_final: 0.7190 (t0) REVERT: b 251 ASP cc_start: 0.7662 (m-30) cc_final: 0.7359 (m-30) REVERT: a 419 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7340 (tt0) REVERT: a 445 MET cc_start: 0.8335 (mtp) cc_final: 0.8077 (mtp) REVERT: A 248 ASP cc_start: 0.7447 (t0) cc_final: 0.7213 (t0) REVERT: C 166 MET cc_start: 0.8850 (mmm) cc_final: 0.8511 (mmm) REVERT: B 140 PHE cc_start: 0.8223 (t80) cc_final: 0.7830 (t80) REVERT: B 378 LYS cc_start: 0.8816 (tttt) cc_final: 0.8569 (tttm) REVERT: B 419 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7305 (tt0) REVERT: B 445 MET cc_start: 0.8316 (mtp) cc_final: 0.8055 (mtp) outliers start: 17 outliers final: 3 residues processed: 236 average time/residue: 0.3286 time to fit residues: 110.8316 Evaluate side-chains 174 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain C residue 404 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN E 166 ASN E 178 HIS ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 38 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 ASN A 166 ASN A 178 HIS ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16792 Z= 0.250 Angle : 0.711 8.558 22848 Z= 0.358 Chirality : 0.045 0.182 2572 Planarity : 0.005 0.046 2966 Dihedral : 6.359 55.863 2363 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.20 % Favored : 86.70 % Rotamer: Outliers : 2.01 % Allowed : 12.03 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.18), residues: 2128 helix: 0.08 (0.20), residues: 732 sheet: -3.15 (0.24), residues: 426 loop : -3.12 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 361 HIS 0.005 0.001 HIS a 215 PHE 0.024 0.002 PHE a 140 TYR 0.014 0.001 TYR C 37 ARG 0.006 0.000 ARG b 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.8357 (mm) cc_final: 0.7938 (mm) REVERT: E 248 ASP cc_start: 0.7345 (t0) cc_final: 0.7131 (t0) REVERT: b 247 ARG cc_start: 0.7201 (ptp-110) cc_final: 0.6951 (ptp-110) REVERT: a 64 GLN cc_start: 0.7654 (tp40) cc_final: 0.7182 (tp40) REVERT: a 419 GLN cc_start: 0.7487 (tp-100) cc_final: 0.7073 (tt0) REVERT: A 62 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7434 (ttm110) REVERT: C 166 MET cc_start: 0.8800 (mmm) cc_final: 0.8478 (mmm) REVERT: C 247 ARG cc_start: 0.7180 (mtm-85) cc_final: 0.6829 (ptp-110) REVERT: C 251 ASP cc_start: 0.7329 (m-30) cc_final: 0.6907 (m-30) REVERT: B 64 GLN cc_start: 0.7334 (tp40) cc_final: 0.6947 (tp40) REVERT: B 419 GLN cc_start: 0.7588 (tp-100) cc_final: 0.7085 (tt0) outliers start: 34 outliers final: 30 residues processed: 220 average time/residue: 0.2796 time to fit residues: 92.1842 Evaluate side-chains 203 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 286 GLN Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 497 GLU 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: 1.9990 chunk 161 optimal weight: 0.2980 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16792 Z= 0.263 Angle : 0.691 8.787 22848 Z= 0.346 Chirality : 0.045 0.179 2572 Planarity : 0.005 0.046 2966 Dihedral : 6.165 53.330 2363 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.33 % Favored : 85.53 % Rotamer: Outliers : 2.84 % Allowed : 13.27 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.62 (0.18), residues: 2128 helix: 0.48 (0.20), residues: 736 sheet: -2.93 (0.24), residues: 426 loop : -3.01 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 361 HIS 0.005 0.001 HIS a 215 PHE 0.027 0.002 PHE B 487 TYR 0.013 0.001 TYR b 37 ARG 0.009 0.000 ARG a 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 181 time to evaluate : 2.040 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 42 SER cc_start: 0.8933 (t) cc_final: 0.8733 (m) REVERT: b 247 ARG cc_start: 0.7254 (ptp-110) cc_final: 0.6939 (ptp-110) REVERT: a 64 GLN cc_start: 0.7702 (tp40) cc_final: 0.7136 (tp40) REVERT: a 419 GLN cc_start: 0.7425 (tp-100) cc_final: 0.7118 (tt0) REVERT: A 31 ILE cc_start: 0.8777 (mm) cc_final: 0.8151 (mt) REVERT: C 166 MET cc_start: 0.8802 (mmm) cc_final: 0.8460 (mmm) REVERT: B 64 GLN cc_start: 0.7395 (tp40) cc_final: 0.6940 (tp40) REVERT: B 419 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7137 (tt0) outliers start: 48 outliers final: 39 residues processed: 216 average time/residue: 0.2848 time to fit residues: 95.1521 Evaluate side-chains 208 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 386 ASP Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 441 GLU Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain a residue 497 GLU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 272 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 30 GLN a 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16792 Z= 0.169 Angle : 0.640 8.075 22848 Z= 0.320 Chirality : 0.043 0.205 2572 Planarity : 0.004 0.045 2966 Dihedral : 5.820 52.877 2363 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.14 % Favored : 88.77 % Rotamer: Outliers : 2.67 % Allowed : 15.05 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.23 (0.19), residues: 2128 helix: 0.78 (0.21), residues: 736 sheet: -2.32 (0.27), residues: 366 loop : -2.98 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 361 HIS 0.005 0.001 HIS a 215 PHE 0.016 0.001 PHE A 27 TYR 0.011 0.001 TYR A 32 ARG 0.008 0.000 ARG a 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 190 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 62 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7301 (ttm110) REVERT: b 166 MET cc_start: 0.8651 (mmm) cc_final: 0.8200 (mmm) REVERT: b 247 ARG cc_start: 0.7232 (ptp-110) cc_final: 0.6926 (ptp-110) REVERT: b 377 LYS cc_start: 0.8371 (tptp) cc_final: 0.8110 (tptp) REVERT: a 64 GLN cc_start: 0.7619 (tp40) cc_final: 0.7051 (tp40) REVERT: A 31 ILE cc_start: 0.8819 (mm) cc_final: 0.8250 (mm) REVERT: C 166 MET cc_start: 0.8812 (mmm) cc_final: 0.8385 (mmm) REVERT: B 64 GLN cc_start: 0.7418 (tp40) cc_final: 0.6889 (tp40) REVERT: B 419 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7093 (tt0) outliers start: 45 outliers final: 37 residues processed: 224 average time/residue: 0.2609 time to fit residues: 89.6987 Evaluate side-chains 210 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 386 ASP Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 220 THR Chi-restraints excluded: chain a residue 286 GLN Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 0.2980 chunk 117 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 185 optimal weight: 0.0970 chunk 52 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 419 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16792 Z= 0.232 Angle : 0.658 8.432 22848 Z= 0.328 Chirality : 0.044 0.208 2572 Planarity : 0.005 0.044 2966 Dihedral : 5.762 52.897 2362 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.16 % Favored : 86.70 % Rotamer: Outliers : 3.26 % Allowed : 14.69 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.23 (0.19), residues: 2128 helix: 0.77 (0.20), residues: 750 sheet: -2.45 (0.26), residues: 412 loop : -2.93 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 361 HIS 0.004 0.001 HIS a 215 PHE 0.029 0.002 PHE a 487 TYR 0.011 0.001 TYR C 37 ARG 0.007 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 166 MET cc_start: 0.8735 (mmm) cc_final: 0.8283 (mmm) REVERT: b 247 ARG cc_start: 0.7217 (ptp-110) cc_final: 0.6859 (ptp-110) REVERT: b 377 LYS cc_start: 0.8349 (tptp) cc_final: 0.8089 (tptp) REVERT: a 64 GLN cc_start: 0.7683 (tp40) cc_final: 0.7067 (tp40) REVERT: a 446 ASP cc_start: 0.7792 (p0) cc_final: 0.7583 (p0) REVERT: A 31 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8176 (mm) REVERT: C 166 MET cc_start: 0.8825 (mmm) cc_final: 0.8412 (mmm) REVERT: C 282 MET cc_start: 0.7775 (mtp) cc_final: 0.7518 (mtt) REVERT: B 64 GLN cc_start: 0.7472 (tp40) cc_final: 0.6921 (tp40) REVERT: B 419 GLN cc_start: 0.7388 (tp-100) cc_final: 0.7119 (tt0) outliers start: 55 outliers final: 44 residues processed: 222 average time/residue: 0.2731 time to fit residues: 93.0048 Evaluate side-chains 219 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 172 HIS Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 386 ASP Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 208 THR Chi-restraints excluded: chain a residue 220 THR Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 458 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 272 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 51 optimal weight: 0.0070 chunk 207 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 419 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16792 Z= 0.238 Angle : 0.660 8.820 22848 Z= 0.328 Chirality : 0.044 0.201 2572 Planarity : 0.005 0.044 2966 Dihedral : 5.767 53.121 2362 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.69 % Favored : 87.22 % Rotamer: Outliers : 3.50 % Allowed : 15.46 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.15 (0.19), residues: 2128 helix: 0.78 (0.20), residues: 758 sheet: -2.35 (0.26), residues: 412 loop : -2.90 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 8 HIS 0.004 0.001 HIS a 215 PHE 0.029 0.002 PHE a 487 TYR 0.012 0.001 TYR C 37 ARG 0.007 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 178 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 166 MET cc_start: 0.8758 (mmm) cc_final: 0.8297 (mmm) REVERT: b 247 ARG cc_start: 0.7256 (ptp-110) cc_final: 0.6647 (ptp-110) REVERT: b 251 ASP cc_start: 0.7566 (m-30) cc_final: 0.7119 (m-30) REVERT: b 377 LYS cc_start: 0.8339 (tptp) cc_final: 0.8085 (tptp) REVERT: a 64 GLN cc_start: 0.7684 (tp40) cc_final: 0.7070 (tp40) REVERT: a 446 ASP cc_start: 0.7794 (p0) cc_final: 0.7548 (p0) REVERT: A 31 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 166 MET cc_start: 0.8865 (mmm) cc_final: 0.8426 (mmm) REVERT: C 282 MET cc_start: 0.7779 (mtp) cc_final: 0.7542 (mtt) REVERT: B 64 GLN cc_start: 0.7458 (tp40) cc_final: 0.6886 (tp40) REVERT: B 419 GLN cc_start: 0.7349 (tp-100) cc_final: 0.7092 (tt0) outliers start: 59 outliers final: 52 residues processed: 221 average time/residue: 0.2619 time to fit residues: 89.4672 Evaluate side-chains 225 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 172 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 386 ASP Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 208 THR Chi-restraints excluded: chain a residue 220 THR Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 458 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 125 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16792 Z= 0.277 Angle : 0.681 10.340 22848 Z= 0.339 Chirality : 0.045 0.227 2572 Planarity : 0.005 0.045 2966 Dihedral : 5.843 53.574 2362 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.00 % Favored : 85.81 % Rotamer: Outliers : 3.14 % Allowed : 16.82 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.16 (0.19), residues: 2128 helix: 0.77 (0.20), residues: 756 sheet: -2.34 (0.26), residues: 422 loop : -2.91 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 328 HIS 0.004 0.001 HIS B 215 PHE 0.030 0.002 PHE a 487 TYR 0.011 0.001 TYR C 37 ARG 0.007 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 179 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 306 LYS cc_start: 0.7838 (pttm) cc_final: 0.7293 (ptpp) REVERT: b 166 MET cc_start: 0.8785 (mmm) cc_final: 0.8342 (mmm) REVERT: b 247 ARG cc_start: 0.7209 (ptp-110) cc_final: 0.6503 (ptp-110) REVERT: b 251 ASP cc_start: 0.7574 (m-30) cc_final: 0.7138 (m-30) REVERT: b 377 LYS cc_start: 0.8330 (tptp) cc_final: 0.8080 (tptp) REVERT: a 64 GLN cc_start: 0.7704 (tp40) cc_final: 0.7087 (tp40) REVERT: a 446 ASP cc_start: 0.7807 (p0) cc_final: 0.7555 (p0) REVERT: A 31 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8274 (mm) REVERT: C 166 MET cc_start: 0.8832 (mmm) cc_final: 0.8428 (mmm) REVERT: C 282 MET cc_start: 0.7762 (mtp) cc_final: 0.7490 (mtt) REVERT: B 64 GLN cc_start: 0.7546 (tp40) cc_final: 0.6980 (tp40) REVERT: B 126 LEU cc_start: 0.5431 (mp) cc_final: 0.5213 (mt) REVERT: B 419 GLN cc_start: 0.7290 (tp-100) cc_final: 0.7049 (tt0) outliers start: 53 outliers final: 51 residues processed: 217 average time/residue: 0.2611 time to fit residues: 87.8683 Evaluate side-chains 224 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 172 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 386 ASP Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 208 THR Chi-restraints excluded: chain a residue 220 THR Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 458 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16792 Z= 0.263 Angle : 0.682 10.083 22848 Z= 0.339 Chirality : 0.045 0.232 2572 Planarity : 0.005 0.052 2966 Dihedral : 5.833 53.990 2362 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.02 % Favored : 86.84 % Rotamer: Outliers : 3.20 % Allowed : 17.71 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.16 (0.19), residues: 2128 helix: 0.79 (0.20), residues: 756 sheet: -2.27 (0.27), residues: 410 loop : -2.96 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 328 HIS 0.005 0.001 HIS B 215 PHE 0.030 0.002 PHE a 487 TYR 0.012 0.001 TYR C 37 ARG 0.013 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 166 MET cc_start: 0.8777 (mmm) cc_final: 0.8333 (mmm) REVERT: b 247 ARG cc_start: 0.7227 (ptp-110) cc_final: 0.6558 (ptp-110) REVERT: b 251 ASP cc_start: 0.7601 (m-30) cc_final: 0.7152 (m-30) REVERT: b 377 LYS cc_start: 0.8327 (tptp) cc_final: 0.8083 (tptp) REVERT: a 64 GLN cc_start: 0.7756 (tp40) cc_final: 0.7122 (tp40) REVERT: a 446 ASP cc_start: 0.7819 (p0) cc_final: 0.7564 (p0) REVERT: A 31 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8324 (mm) REVERT: C 166 MET cc_start: 0.8839 (mmm) cc_final: 0.8425 (mmm) REVERT: C 282 MET cc_start: 0.7752 (mtp) cc_final: 0.7488 (mtt) REVERT: B 64 GLN cc_start: 0.7555 (tp40) cc_final: 0.6964 (tp40) REVERT: B 126 LEU cc_start: 0.5231 (mp) cc_final: 0.5016 (mt) REVERT: B 419 GLN cc_start: 0.7278 (tp-100) cc_final: 0.7030 (tt0) outliers start: 54 outliers final: 53 residues processed: 219 average time/residue: 0.2570 time to fit residues: 88.1312 Evaluate side-chains 228 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 386 ASP Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 208 THR Chi-restraints excluded: chain a residue 220 THR Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 458 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 465 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16792 Z= 0.253 Angle : 0.681 11.113 22848 Z= 0.338 Chirality : 0.044 0.232 2572 Planarity : 0.005 0.051 2966 Dihedral : 5.800 54.353 2362 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.53 % Favored : 86.33 % Rotamer: Outliers : 3.08 % Allowed : 18.25 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.12 (0.19), residues: 2128 helix: 0.82 (0.20), residues: 756 sheet: -2.25 (0.27), residues: 420 loop : -2.93 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 328 HIS 0.005 0.001 HIS a 215 PHE 0.029 0.001 PHE a 487 TYR 0.010 0.001 TYR C 37 ARG 0.015 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 178 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 306 LYS cc_start: 0.7916 (pttm) cc_final: 0.7310 (ptpp) REVERT: b 166 MET cc_start: 0.8783 (mmm) cc_final: 0.8330 (mmm) REVERT: b 247 ARG cc_start: 0.7233 (ptp-110) cc_final: 0.6557 (ptp-110) REVERT: b 251 ASP cc_start: 0.7600 (m-30) cc_final: 0.7150 (m-30) REVERT: b 377 LYS cc_start: 0.8319 (tptp) cc_final: 0.8075 (tptp) REVERT: a 64 GLN cc_start: 0.7737 (tp40) cc_final: 0.7098 (tp40) REVERT: a 446 ASP cc_start: 0.7822 (p0) cc_final: 0.7565 (p0) REVERT: A 31 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8364 (mm) REVERT: C 166 MET cc_start: 0.8830 (mmm) cc_final: 0.8409 (mmm) REVERT: C 282 MET cc_start: 0.7745 (mtp) cc_final: 0.7507 (mtt) REVERT: C 377 LYS cc_start: 0.8366 (tptp) cc_final: 0.8119 (tptp) REVERT: B 64 GLN cc_start: 0.7567 (tp40) cc_final: 0.6958 (tp40) REVERT: B 419 GLN cc_start: 0.7277 (tp-100) cc_final: 0.7025 (tt0) outliers start: 52 outliers final: 49 residues processed: 214 average time/residue: 0.2584 time to fit residues: 85.6479 Evaluate side-chains 223 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 242 LEU Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 386 ASP Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 208 THR Chi-restraints excluded: chain a residue 220 THR Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 458 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 141 optimal weight: 0.3980 chunk 213 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 169 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16792 Z= 0.198 Angle : 0.660 10.272 22848 Z= 0.327 Chirality : 0.043 0.229 2572 Planarity : 0.005 0.051 2966 Dihedral : 5.666 54.147 2362 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.75 % Favored : 88.11 % Rotamer: Outliers : 2.61 % Allowed : 18.96 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.00 (0.19), residues: 2128 helix: 0.90 (0.21), residues: 756 sheet: -2.07 (0.28), residues: 392 loop : -2.91 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 328 HIS 0.005 0.001 HIS a 215 PHE 0.028 0.001 PHE a 487 TYR 0.010 0.001 TYR E 240 ARG 0.017 0.000 ARG E 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 306 LYS cc_start: 0.7908 (pttm) cc_final: 0.7336 (ptpp) REVERT: b 166 MET cc_start: 0.8794 (mmm) cc_final: 0.8319 (mmm) REVERT: b 247 ARG cc_start: 0.7233 (ptp-110) cc_final: 0.6889 (ptp-110) REVERT: b 377 LYS cc_start: 0.8331 (tptp) cc_final: 0.8092 (tptp) REVERT: a 64 GLN cc_start: 0.7742 (tp40) cc_final: 0.7100 (tp40) REVERT: a 446 ASP cc_start: 0.7786 (p0) cc_final: 0.7535 (p0) REVERT: A 31 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8311 (mm) REVERT: C 166 MET cc_start: 0.8821 (mmm) cc_final: 0.8377 (mmm) REVERT: C 377 LYS cc_start: 0.8372 (tptp) cc_final: 0.8121 (tptp) REVERT: B 64 GLN cc_start: 0.7613 (tp40) cc_final: 0.7005 (tp40) outliers start: 44 outliers final: 43 residues processed: 210 average time/residue: 0.2495 time to fit residues: 81.8618 Evaluate side-chains 215 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 171 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain b residue 12 PHE Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 281 LEU Chi-restraints excluded: chain b residue 314 VAL Chi-restraints excluded: chain b residue 357 VAL Chi-restraints excluded: chain b residue 366 THR Chi-restraints excluded: chain b residue 386 ASP Chi-restraints excluded: chain b residue 404 VAL Chi-restraints excluded: chain a residue 183 TYR Chi-restraints excluded: chain a residue 189 THR Chi-restraints excluded: chain a residue 220 THR Chi-restraints excluded: chain a residue 234 ASP Chi-restraints excluded: chain a residue 272 HIS Chi-restraints excluded: chain a residue 395 VAL Chi-restraints excluded: chain a residue 465 ILE Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 458 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: 5.9990 chunk 156 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 149 optimal weight: 0.3980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN ** a 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107958 restraints weight = 28251.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110750 restraints weight = 17500.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112601 restraints weight = 12998.020| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16792 Z= 0.194 Angle : 0.652 10.347 22848 Z= 0.324 Chirality : 0.043 0.228 2572 Planarity : 0.005 0.063 2966 Dihedral : 5.579 53.859 2362 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.41 % Favored : 87.45 % Rotamer: Outliers : 2.43 % Allowed : 19.55 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.96 (0.19), residues: 2128 helix: 0.89 (0.20), residues: 768 sheet: -1.99 (0.28), residues: 392 loop : -2.92 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 328 HIS 0.005 0.001 HIS a 215 PHE 0.026 0.001 PHE a 487 TYR 0.009 0.001 TYR b 37 ARG 0.016 0.000 ARG E 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.53 seconds wall clock time: 53 minutes 4.35 seconds (3184.35 seconds total)