Starting phenix.real_space_refine on Sat Mar 16 15:08:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/03_2024/6m67_30115.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/03_2024/6m67_30115.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/6m67_30115/03_2024/6m67_30115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/03_2024/6m67_30115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/03_2024/6m67_30115.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/03_2024/6m67_30115.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= 0.201 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 70 5.16 5 C 9975 2.51 5 N 2303 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14938 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "B" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "C" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "D" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "E" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "F" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "G" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Time building chain proxies: 7.18, per 1000 atoms: 0.48 Number of scatterers: 14938 At special positions: 0 Unit cell: (112.042, 112.042, 117.327, 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 70 16.00 O 2590 8.00 N 2303 7.00 C 9975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.04 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.04 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.04 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.04 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.04 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.04 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.10 Conformation dependent library (CDL) restraints added in 2.3 seconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 7 sheets defined 72.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 4.020A pdb=" N ILE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.739A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 107 " --> pdb=" O TRP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 108 through 131 removed outlier: 3.766A pdb=" N LEU A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 156 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 294 through 300 removed outlier: 5.063A pdb=" N VAL A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Proline residue: A 298 - end of helix No H-bonds generated for 'chain 'A' and resid 294 through 300' Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.738A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 107 " --> pdb=" O TRP B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 108 through 131 removed outlier: 3.766A pdb=" N LEU B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.099A pdb=" N ASN B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 294 through 300 removed outlier: 5.063A pdb=" N VAL B 297 " --> pdb=" O THR B 294 " (cutoff:3.500A) Proline residue: B 298 - end of helix No H-bonds generated for 'chain 'B' and resid 294 through 300' Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.738A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 107 " --> pdb=" O TRP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 108 through 131 removed outlier: 3.765A pdb=" N LEU C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 156 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 238 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 286 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 294 through 300 removed outlier: 5.063A pdb=" N VAL C 297 " --> pdb=" O THR C 294 " (cutoff:3.500A) Proline residue: C 298 - end of helix No H-bonds generated for 'chain 'C' and resid 294 through 300' Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.739A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 107 " --> pdb=" O TRP D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 107' Processing helix chain 'D' and resid 108 through 131 removed outlier: 3.766A pdb=" N LEU D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 156 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.681A pdb=" N LYS D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 210 through 238 removed outlier: 4.787A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 238 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 286 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 294 through 300 removed outlier: 5.064A pdb=" N VAL D 297 " --> pdb=" O THR D 294 " (cutoff:3.500A) Proline residue: D 298 - end of helix No H-bonds generated for 'chain 'D' and resid 294 through 300' Processing helix chain 'D' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 320 Processing helix chain 'D' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.739A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 103 through 107 removed outlier: 4.529A pdb=" N HIS E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 107 " --> pdb=" O TRP E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 107' Processing helix chain 'E' and resid 108 through 131 removed outlier: 3.766A pdb=" N LEU E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 156 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 238 " --> pdb=" O TYR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 256 removed outlier: 4.099A pdb=" N ASN E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 274 Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 286 Processing helix chain 'E' and resid 287 through 293 Processing helix chain 'E' and resid 294 through 300 removed outlier: 5.064A pdb=" N VAL E 297 " --> pdb=" O THR E 294 " (cutoff:3.500A) Proline residue: E 298 - end of helix No H-bonds generated for 'chain 'E' and resid 294 through 300' Processing helix chain 'E' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 59 removed outlier: 4.020A pdb=" N ILE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.738A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS F 107 " --> pdb=" O TRP F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 107' Processing helix chain 'F' and resid 108 through 131 removed outlier: 3.765A pdb=" N LEU F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 156 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS F 203 " --> pdb=" O TYR F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 218 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 238 " --> pdb=" O TYR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN F 255 " --> pdb=" O GLY F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 274 Processing helix chain 'F' and resid 275 through 277 No H-bonds generated for 'chain 'F' and resid 275 through 277' Processing helix chain 'F' and resid 278 through 286 Processing helix chain 'F' and resid 287 through 293 Processing helix chain 'F' and resid 294 through 300 removed outlier: 5.064A pdb=" N VAL F 297 " --> pdb=" O THR F 294 " (cutoff:3.500A) Proline residue: F 298 - end of helix No H-bonds generated for 'chain 'F' and resid 294 through 300' Processing helix chain 'F' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.738A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G 107 " --> pdb=" O TRP G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 107' Processing helix chain 'G' and resid 108 through 131 removed outlier: 3.765A pdb=" N LEU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 156 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS G 203 " --> pdb=" O TYR G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'G' and resid 210 through 238 removed outlier: 4.787A pdb=" N CYS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER G 238 " --> pdb=" O TYR G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN G 255 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 274 Processing helix chain 'G' and resid 275 through 277 No H-bonds generated for 'chain 'G' and resid 275 through 277' Processing helix chain 'G' and resid 278 through 286 Processing helix chain 'G' and resid 287 through 293 Processing helix chain 'G' and resid 294 through 300 removed outlier: 5.063A pdb=" N VAL G 297 " --> pdb=" O THR G 294 " (cutoff:3.500A) Proline residue: G 298 - end of helix No H-bonds generated for 'chain 'G' and resid 294 through 300' Processing helix chain 'G' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 320 Processing helix chain 'G' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER A 65 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.522A pdb=" N SER B 65 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER C 65 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER D 65 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER E 65 " --> pdb=" O LYS E 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER F 65 " --> pdb=" O LYS F 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER G 65 " --> pdb=" O LYS G 266 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4336 1.34 - 1.46: 3078 1.46 - 1.57: 7811 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15309 Sorted by residual: bond pdb=" C PRO A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.74e+00 bond pdb=" C PRO C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.36e-02 5.41e+03 2.74e+00 bond pdb=" C PRO B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.36e-02 5.41e+03 2.65e+00 bond pdb=" C PRO G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.64e+00 bond pdb=" C PRO F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.61e+00 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.42: 512 107.42 - 114.09: 8507 114.09 - 120.75: 7066 120.75 - 127.41: 4564 127.41 - 134.08: 176 Bond angle restraints: 20825 Sorted by residual: angle pdb=" N THR D 314 " pdb=" CA THR D 314 " pdb=" C THR D 314 " ideal model delta sigma weight residual 114.56 108.03 6.53 1.27e+00 6.20e-01 2.65e+01 angle pdb=" N THR B 314 " pdb=" CA THR B 314 " pdb=" C THR B 314 " ideal model delta sigma weight residual 114.56 108.04 6.52 1.27e+00 6.20e-01 2.64e+01 angle pdb=" N THR C 314 " pdb=" CA THR C 314 " pdb=" C THR C 314 " ideal model delta sigma weight residual 114.56 108.04 6.52 1.27e+00 6.20e-01 2.63e+01 angle pdb=" N THR F 314 " pdb=" CA THR F 314 " pdb=" C THR F 314 " ideal model delta sigma weight residual 114.56 108.05 6.51 1.27e+00 6.20e-01 2.63e+01 angle pdb=" N THR A 314 " pdb=" CA THR A 314 " pdb=" C THR A 314 " ideal model delta sigma weight residual 114.56 108.05 6.51 1.27e+00 6.20e-01 2.63e+01 ... (remaining 20820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.17: 6873 10.17 - 20.35: 1296 20.35 - 30.52: 560 30.52 - 40.70: 315 40.70 - 50.87: 70 Dihedral angle restraints: 9114 sinusoidal: 3563 harmonic: 5551 Sorted by residual: dihedral pdb=" CA LYS D 107 " pdb=" C LYS D 107 " pdb=" N PHE D 108 " pdb=" CA PHE D 108 " ideal model delta harmonic sigma weight residual 180.00 -151.71 -28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS F 107 " pdb=" C LYS F 107 " pdb=" N PHE F 108 " pdb=" CA PHE F 108 " ideal model delta harmonic sigma weight residual 180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS B 107 " pdb=" C LYS B 107 " pdb=" N PHE B 108 " pdb=" CA PHE B 108 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1619 0.051 - 0.103: 649 0.103 - 0.154: 159 0.154 - 0.206: 37 0.206 - 0.257: 7 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA PHE B 109 " pdb=" N PHE B 109 " pdb=" C PHE B 109 " pdb=" CB PHE B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PHE F 109 " pdb=" N PHE F 109 " pdb=" C PHE F 109 " pdb=" CB PHE F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PHE E 109 " pdb=" N PHE E 109 " pdb=" C PHE E 109 " pdb=" CB PHE E 109 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2468 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 312 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO B 313 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 312 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO C 313 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 313 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 312 " 0.050 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO G 313 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO G 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 313 " 0.041 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3522 2.78 - 3.31: 13875 3.31 - 3.84: 25008 3.84 - 4.37: 27524 4.37 - 4.90: 44939 Nonbonded interactions: 114868 Sorted by model distance: nonbonded pdb=" O PHE A 72 " pdb=" OG SER B 71 " model vdw 2.247 2.440 nonbonded pdb=" O PHE F 72 " pdb=" OG SER G 71 " model vdw 2.248 2.440 nonbonded pdb=" OG SER A 71 " pdb=" O PHE G 72 " model vdw 2.285 2.440 nonbonded pdb=" O SER B 241 " pdb=" OG SER B 241 " model vdw 2.300 2.440 nonbonded pdb=" O SER C 241 " pdb=" OG SER C 241 " model vdw 2.300 2.440 ... (remaining 114863 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.940 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: 4.220 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 36.430 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15309 Z= 0.352 Angle : 1.137 9.158 20825 Z= 0.599 Chirality : 0.059 0.257 2471 Planarity : 0.010 0.075 2520 Dihedral : 14.949 50.872 5460 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.16), residues: 1827 helix: -3.29 (0.10), residues: 1141 sheet: None (None), residues: 0 loop : -2.81 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.008 0.003 HIS A 106 PHE 0.028 0.002 PHE A 109 TYR 0.015 0.002 TYR E 234 ARG 0.008 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7104 (mt0) cc_final: 0.6873 (mt0) REVERT: A 75 ARG cc_start: 0.7158 (tpp-160) cc_final: 0.6899 (ttt90) REVERT: A 214 ILE cc_start: 0.6695 (tp) cc_final: 0.6422 (mp) REVERT: B 242 ASP cc_start: 0.7776 (t70) cc_final: 0.7389 (m-30) REVERT: C 83 TYR cc_start: 0.7734 (t80) cc_final: 0.7192 (t80) REVERT: C 214 ILE cc_start: 0.6891 (tp) cc_final: 0.6659 (pt) REVERT: C 242 ASP cc_start: 0.7566 (t70) cc_final: 0.7241 (m-30) REVERT: D 83 TYR cc_start: 0.7572 (t80) cc_final: 0.6937 (t80) REVERT: D 214 ILE cc_start: 0.7314 (tp) cc_final: 0.7037 (mt) REVERT: D 242 ASP cc_start: 0.7656 (t70) cc_final: 0.7298 (m-30) REVERT: D 262 GLN cc_start: 0.7828 (pm20) cc_final: 0.7572 (pp30) REVERT: D 279 ILE cc_start: 0.8170 (mt) cc_final: 0.7906 (mt) REVERT: E 83 TYR cc_start: 0.7590 (t80) cc_final: 0.7356 (t80) REVERT: E 214 ILE cc_start: 0.6888 (tp) cc_final: 0.6578 (pt) REVERT: E 242 ASP cc_start: 0.7434 (t70) cc_final: 0.7195 (m-30) REVERT: F 279 ILE cc_start: 0.8288 (mt) cc_final: 0.8033 (mt) REVERT: G 124 PRO cc_start: 0.9038 (Cg_exo) cc_final: 0.8753 (Cg_endo) REVERT: G 199 TYR cc_start: 0.7883 (m-80) cc_final: 0.7659 (m-10) REVERT: G 214 ILE cc_start: 0.7012 (tp) cc_final: 0.6704 (mt) REVERT: G 299 PHE cc_start: 0.7160 (t80) cc_final: 0.6938 (t80) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2566 time to fit residues: 147.5613 Evaluate side-chains 243 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A 280 ASN B 56 GLN B 90 GLN B 280 ASN C 56 GLN C 76 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 280 ASN F 56 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN G 280 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15309 Z= 0.207 Angle : 0.784 10.002 20825 Z= 0.395 Chirality : 0.045 0.205 2471 Planarity : 0.007 0.058 2520 Dihedral : 6.486 23.295 1981 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.90 % Allowed : 18.49 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.18), residues: 1827 helix: -1.56 (0.14), residues: 1113 sheet: -2.83 (0.42), residues: 84 loop : -3.59 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 127 HIS 0.003 0.001 HIS F 106 PHE 0.028 0.002 PHE D 299 TYR 0.026 0.002 TYR E 121 ARG 0.003 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 284 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.9007 (mt) cc_final: 0.8332 (tt) REVERT: C 57 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8258 (mm-30) REVERT: C 90 GLN cc_start: 0.6755 (tt0) cc_final: 0.6402 (mt0) REVERT: C 119 LEU cc_start: 0.8762 (mp) cc_final: 0.8035 (tt) REVERT: D 119 LEU cc_start: 0.8937 (mt) cc_final: 0.8141 (tt) REVERT: D 127 TRP cc_start: 0.7730 (t60) cc_final: 0.7396 (t60) REVERT: D 262 GLN cc_start: 0.7665 (pm20) cc_final: 0.7433 (pp30) REVERT: D 279 ILE cc_start: 0.8141 (mt) cc_final: 0.7851 (mt) REVERT: D 299 PHE cc_start: 0.6632 (t80) cc_final: 0.6351 (t80) REVERT: E 119 LEU cc_start: 0.8718 (mp) cc_final: 0.8010 (tt) REVERT: F 199 TYR cc_start: 0.7147 (m-10) cc_final: 0.6875 (m-10) REVERT: F 279 ILE cc_start: 0.8209 (mt) cc_final: 0.7917 (mt) REVERT: G 124 PRO cc_start: 0.9043 (Cg_exo) cc_final: 0.8709 (Cg_endo) REVERT: G 128 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7856 (mtp-110) REVERT: G 199 TYR cc_start: 0.7850 (m-80) cc_final: 0.7629 (m-10) REVERT: G 214 ILE cc_start: 0.6991 (tp) cc_final: 0.6780 (mt) REVERT: G 307 LYS cc_start: 0.7725 (mptt) cc_final: 0.7516 (mptt) outliers start: 32 outliers final: 7 residues processed: 308 average time/residue: 0.2429 time to fit residues: 113.1887 Evaluate side-chains 234 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 242 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 178 optimal weight: 0.0010 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN G 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15309 Z= 0.210 Angle : 0.754 9.788 20825 Z= 0.375 Chirality : 0.045 0.197 2471 Planarity : 0.006 0.051 2520 Dihedral : 5.935 21.191 1981 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.90 % Allowed : 22.11 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.19), residues: 1827 helix: -0.65 (0.15), residues: 1113 sheet: -1.92 (0.48), residues: 84 loop : -3.44 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 85 HIS 0.004 0.001 HIS G 106 PHE 0.021 0.002 PHE F 299 TYR 0.027 0.002 TYR E 121 ARG 0.003 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 243 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.4670 (OUTLIER) cc_final: 0.2080 (mt) REVERT: A 119 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8261 (tt) REVERT: B 103 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.1964 (mt) REVERT: C 57 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8110 (mm-30) REVERT: C 83 TYR cc_start: 0.7692 (t80) cc_final: 0.7403 (t80) REVERT: C 262 GLN cc_start: 0.7456 (pm20) cc_final: 0.7216 (pp30) REVERT: C 274 GLN cc_start: 0.8026 (tt0) cc_final: 0.7816 (tt0) REVERT: D 119 LEU cc_start: 0.8949 (mt) cc_final: 0.8265 (tt) REVERT: D 262 GLN cc_start: 0.7746 (pm20) cc_final: 0.7344 (pp30) REVERT: D 299 PHE cc_start: 0.6786 (t80) cc_final: 0.6500 (t80) REVERT: E 119 LEU cc_start: 0.8729 (mp) cc_final: 0.8044 (tt) REVERT: E 214 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6372 (pt) REVERT: F 57 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8162 (mm-30) REVERT: F 103 LEU cc_start: 0.4952 (OUTLIER) cc_final: 0.2348 (mt) REVERT: F 199 TYR cc_start: 0.7297 (m-10) cc_final: 0.6915 (m-10) REVERT: G 103 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.2288 (mt) REVERT: G 128 ARG cc_start: 0.8406 (ttm110) cc_final: 0.7890 (mtp-110) outliers start: 49 outliers final: 28 residues processed: 275 average time/residue: 0.2460 time to fit residues: 102.0672 Evaluate side-chains 247 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 0.0030 chunk 79 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15309 Z= 0.165 Angle : 0.714 9.816 20825 Z= 0.352 Chirality : 0.043 0.178 2471 Planarity : 0.005 0.048 2520 Dihedral : 5.518 19.106 1981 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.68 % Allowed : 24.30 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.20), residues: 1827 helix: -0.30 (0.16), residues: 1155 sheet: -1.92 (0.48), residues: 84 loop : -3.19 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 85 HIS 0.002 0.001 HIS F 106 PHE 0.019 0.001 PHE A 320 TYR 0.025 0.001 TYR C 121 ARG 0.003 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 254 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8091 (mm-30) REVERT: A 103 LEU cc_start: 0.4515 (OUTLIER) cc_final: 0.2053 (mt) REVERT: A 119 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8196 (tt) REVERT: A 128 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7535 (ttm170) REVERT: B 57 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 103 LEU cc_start: 0.4597 (OUTLIER) cc_final: 0.2081 (mt) REVERT: C 57 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8103 (mm-30) REVERT: C 274 GLN cc_start: 0.7960 (tt0) cc_final: 0.7696 (tt0) REVERT: C 310 GLU cc_start: 0.6383 (mt-10) cc_final: 0.5824 (pm20) REVERT: D 262 GLN cc_start: 0.7661 (pm20) cc_final: 0.7310 (pp30) REVERT: D 299 PHE cc_start: 0.6729 (t80) cc_final: 0.6434 (t80) REVERT: E 119 LEU cc_start: 0.8704 (mp) cc_final: 0.8051 (tt) REVERT: E 214 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6415 (pt) REVERT: F 57 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8139 (mm-30) REVERT: F 103 LEU cc_start: 0.4756 (OUTLIER) cc_final: 0.2152 (mt) REVERT: F 199 TYR cc_start: 0.7375 (m-10) cc_final: 0.6882 (m-10) REVERT: F 226 LEU cc_start: 0.8427 (mm) cc_final: 0.8100 (tt) REVERT: F 272 ILE cc_start: 0.7797 (pt) cc_final: 0.7539 (tp) REVERT: F 274 GLN cc_start: 0.7644 (tt0) cc_final: 0.7404 (tt0) REVERT: F 279 ILE cc_start: 0.8025 (mm) cc_final: 0.7824 (mt) REVERT: G 119 LEU cc_start: 0.9243 (mm) cc_final: 0.8581 (tt) REVERT: G 128 ARG cc_start: 0.8384 (ttm110) cc_final: 0.7852 (mtp-110) REVERT: G 199 TYR cc_start: 0.7017 (m-10) cc_final: 0.6445 (m-80) REVERT: G 226 LEU cc_start: 0.8535 (mm) cc_final: 0.8044 (tt) REVERT: G 299 PHE cc_start: 0.7039 (t80) cc_final: 0.6712 (t80) outliers start: 62 outliers final: 25 residues processed: 294 average time/residue: 0.2417 time to fit residues: 107.3340 Evaluate side-chains 249 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.0170 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 150 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15309 Z= 0.227 Angle : 0.753 10.947 20825 Z= 0.371 Chirality : 0.045 0.187 2471 Planarity : 0.005 0.041 2520 Dihedral : 5.553 19.262 1981 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 4.56 % Allowed : 25.67 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1827 helix: -0.13 (0.16), residues: 1155 sheet: -1.33 (0.55), residues: 70 loop : -3.16 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 127 HIS 0.003 0.001 HIS A 106 PHE 0.030 0.001 PHE F 299 TYR 0.027 0.002 TYR C 121 ARG 0.004 0.001 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 237 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8130 (mm-30) REVERT: A 103 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.2507 (mt) REVERT: A 119 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 128 ARG cc_start: 0.7930 (ttt-90) cc_final: 0.7526 (ttm170) REVERT: B 57 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8149 (mm-30) REVERT: B 103 LEU cc_start: 0.5163 (OUTLIER) cc_final: 0.2571 (mt) REVERT: B 262 GLN cc_start: 0.7670 (pm20) cc_final: 0.7266 (pp30) REVERT: C 57 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8185 (mm-30) REVERT: C 109 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7044 (t80) REVERT: C 274 GLN cc_start: 0.7970 (tt0) cc_final: 0.7681 (tt0) REVERT: C 310 GLU cc_start: 0.6531 (mt-10) cc_final: 0.5996 (pm20) REVERT: D 262 GLN cc_start: 0.7686 (pm20) cc_final: 0.7276 (pp30) REVERT: E 83 TYR cc_start: 0.7505 (t80) cc_final: 0.7301 (t80) REVERT: E 214 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6344 (pt) REVERT: E 243 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6316 (mm-30) REVERT: F 85 TRP cc_start: 0.8124 (t60) cc_final: 0.7422 (t60) REVERT: F 103 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.2421 (mt) REVERT: F 109 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7338 (t80) REVERT: F 226 LEU cc_start: 0.8610 (mm) cc_final: 0.8252 (tt) REVERT: F 274 GLN cc_start: 0.7666 (tt0) cc_final: 0.7437 (tt0) REVERT: G 103 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.2347 (mt) REVERT: G 128 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7879 (mtp-110) REVERT: G 199 TYR cc_start: 0.7178 (m-10) cc_final: 0.6752 (m-10) REVERT: G 226 LEU cc_start: 0.8706 (mm) cc_final: 0.8250 (tt) outliers start: 77 outliers final: 43 residues processed: 293 average time/residue: 0.2577 time to fit residues: 114.7028 Evaluate side-chains 265 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 213 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 103 optimal weight: 0.0010 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN G 56 GLN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15309 Z= 0.171 Angle : 0.713 10.371 20825 Z= 0.350 Chirality : 0.043 0.159 2471 Planarity : 0.005 0.043 2520 Dihedral : 5.315 17.930 1981 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.27 % Allowed : 27.39 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1827 helix: 0.01 (0.16), residues: 1162 sheet: -1.92 (0.50), residues: 84 loop : -3.25 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 127 HIS 0.003 0.001 HIS F 106 PHE 0.023 0.001 PHE F 273 TYR 0.027 0.001 TYR C 121 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 235 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8146 (mm-30) REVERT: A 103 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.2610 (mt) REVERT: A 119 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 128 ARG cc_start: 0.7919 (ttt-90) cc_final: 0.7443 (ttm170) REVERT: A 129 PHE cc_start: 0.8328 (m-10) cc_final: 0.8123 (m-10) REVERT: B 57 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8168 (mm-30) REVERT: B 103 LEU cc_start: 0.4801 (OUTLIER) cc_final: 0.2203 (mt) REVERT: B 120 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 237 LEU cc_start: 0.7374 (tt) cc_final: 0.7049 (tp) REVERT: B 262 GLN cc_start: 0.7588 (pm20) cc_final: 0.7214 (pp30) REVERT: B 272 ILE cc_start: 0.8111 (pt) cc_final: 0.7881 (tp) REVERT: C 57 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8211 (mm-30) REVERT: C 109 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.6906 (t80) REVERT: C 274 GLN cc_start: 0.7923 (tt0) cc_final: 0.7681 (tt0) REVERT: C 310 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6162 (pm20) REVERT: D 262 GLN cc_start: 0.7578 (pm20) cc_final: 0.7248 (pp30) REVERT: D 272 ILE cc_start: 0.8167 (pt) cc_final: 0.7910 (tp) REVERT: D 274 GLN cc_start: 0.7710 (tt0) cc_final: 0.7432 (tt0) REVERT: D 299 PHE cc_start: 0.6515 (t80) cc_final: 0.6303 (t80) REVERT: E 63 GLN cc_start: 0.6024 (tp40) cc_final: 0.5578 (mp10) REVERT: E 103 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.2887 (mt) REVERT: F 85 TRP cc_start: 0.8054 (t60) cc_final: 0.7413 (t60) REVERT: F 109 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7035 (t80) REVERT: F 226 LEU cc_start: 0.8588 (mm) cc_final: 0.8284 (tt) REVERT: G 103 LEU cc_start: 0.4677 (OUTLIER) cc_final: 0.2056 (mt) REVERT: G 128 ARG cc_start: 0.8442 (ttm110) cc_final: 0.7882 (mtp-110) REVERT: G 199 TYR cc_start: 0.7294 (m-10) cc_final: 0.6824 (m-10) REVERT: G 226 LEU cc_start: 0.8722 (mm) cc_final: 0.8279 (tt) REVERT: G 299 PHE cc_start: 0.7021 (t80) cc_final: 0.6729 (t80) outliers start: 72 outliers final: 41 residues processed: 288 average time/residue: 0.2483 time to fit residues: 106.8854 Evaluate side-chains 264 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 214 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 319 HIS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN F 90 GLN F 274 GLN G 56 GLN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15309 Z= 0.209 Angle : 0.737 10.705 20825 Z= 0.363 Chirality : 0.045 0.279 2471 Planarity : 0.005 0.041 2520 Dihedral : 5.358 20.652 1981 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.45 % Allowed : 26.73 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1827 helix: 0.07 (0.16), residues: 1155 sheet: -1.18 (0.59), residues: 70 loop : -3.23 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 85 HIS 0.003 0.001 HIS B 106 PHE 0.030 0.001 PHE F 299 TYR 0.026 0.001 TYR C 121 ARG 0.003 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 223 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8139 (mttm) cc_final: 0.7824 (pttm) REVERT: A 57 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 103 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.2766 (mt) REVERT: A 119 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 128 ARG cc_start: 0.7894 (ttt-90) cc_final: 0.7461 (ttm170) REVERT: A 129 PHE cc_start: 0.8314 (m-10) cc_final: 0.8102 (m-10) REVERT: A 148 LYS cc_start: 0.8213 (tptp) cc_final: 0.7697 (mmmt) REVERT: B 57 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8140 (mm-30) REVERT: B 103 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.2537 (mt) REVERT: B 237 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7127 (tp) REVERT: B 262 GLN cc_start: 0.7623 (pm20) cc_final: 0.7263 (pp30) REVERT: B 272 ILE cc_start: 0.8179 (pt) cc_final: 0.7894 (tp) REVERT: C 57 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8204 (mm-30) REVERT: C 109 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7079 (t80) REVERT: C 274 GLN cc_start: 0.7956 (tt0) cc_final: 0.7718 (tt0) REVERT: C 310 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6196 (pm20) REVERT: D 262 GLN cc_start: 0.7673 (pm20) cc_final: 0.7252 (pp30) REVERT: D 272 ILE cc_start: 0.8220 (pt) cc_final: 0.7909 (tp) REVERT: D 299 PHE cc_start: 0.6523 (t80) cc_final: 0.6182 (t80) REVERT: E 63 GLN cc_start: 0.5977 (tp40) cc_final: 0.5562 (mp10) REVERT: E 101 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5944 (pp) REVERT: E 103 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.3150 (mt) REVERT: E 109 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7428 (t80) REVERT: E 243 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6260 (mm-30) REVERT: E 276 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7223 (tt) REVERT: F 103 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.2434 (mt) REVERT: F 109 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7394 (t80) REVERT: F 226 LEU cc_start: 0.8635 (mm) cc_final: 0.8321 (tt) REVERT: G 103 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.2348 (mt) REVERT: G 128 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7881 (mtp-110) REVERT: G 199 TYR cc_start: 0.7407 (m-10) cc_final: 0.6925 (m-10) REVERT: G 226 LEU cc_start: 0.8745 (mm) cc_final: 0.8305 (tt) outliers start: 92 outliers final: 61 residues processed: 294 average time/residue: 0.2446 time to fit residues: 107.6777 Evaluate side-chains 282 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 207 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 319 HIS Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15309 Z= 0.177 Angle : 0.722 10.953 20825 Z= 0.352 Chirality : 0.044 0.157 2471 Planarity : 0.005 0.040 2520 Dihedral : 5.198 18.514 1981 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.04 % Allowed : 27.92 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1827 helix: 0.12 (0.16), residues: 1169 sheet: -1.19 (0.59), residues: 70 loop : -3.19 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 85 HIS 0.002 0.001 HIS B 106 PHE 0.015 0.001 PHE B 109 TYR 0.026 0.001 TYR E 121 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 220 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8154 (mttm) cc_final: 0.7818 (pttm) REVERT: A 57 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 101 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5918 (pt) REVERT: A 103 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.2817 (mt) REVERT: A 119 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 128 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7347 (ttm170) REVERT: A 129 PHE cc_start: 0.8312 (m-10) cc_final: 0.8076 (m-10) REVERT: A 148 LYS cc_start: 0.8207 (tptp) cc_final: 0.7670 (mmmt) REVERT: B 57 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8126 (mm-30) REVERT: B 101 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5446 (pp) REVERT: B 103 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.2414 (mt) REVERT: B 237 LEU cc_start: 0.7395 (tt) cc_final: 0.7192 (tp) REVERT: B 262 GLN cc_start: 0.7581 (pm20) cc_final: 0.7248 (pp30) REVERT: B 272 ILE cc_start: 0.8013 (pt) cc_final: 0.7806 (tp) REVERT: C 57 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8162 (mm-30) REVERT: C 109 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7016 (t80) REVERT: C 274 GLN cc_start: 0.7934 (tt0) cc_final: 0.7710 (tt0) REVERT: C 310 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6230 (pm20) REVERT: D 103 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.3032 (mt) REVERT: D 262 GLN cc_start: 0.7643 (pm20) cc_final: 0.7309 (pp30) REVERT: D 299 PHE cc_start: 0.6575 (t80) cc_final: 0.6168 (t80) REVERT: E 63 GLN cc_start: 0.5995 (tp40) cc_final: 0.5578 (mp10) REVERT: E 101 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5842 (pp) REVERT: E 103 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.2908 (mt) REVERT: E 109 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7377 (t80) REVERT: E 243 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6225 (mm-30) REVERT: E 276 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6963 (tt) REVERT: F 101 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5757 (pp) REVERT: F 103 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.2412 (mt) REVERT: F 109 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7258 (t80) REVERT: F 226 LEU cc_start: 0.8629 (mm) cc_final: 0.8316 (tt) REVERT: G 103 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.2215 (mt) REVERT: G 109 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.6846 (t80) REVERT: G 128 ARG cc_start: 0.8414 (ttm110) cc_final: 0.7856 (mtp-110) REVERT: G 199 TYR cc_start: 0.7292 (m-10) cc_final: 0.6838 (m-10) REVERT: G 226 LEU cc_start: 0.8709 (mm) cc_final: 0.8244 (tt) outliers start: 85 outliers final: 54 residues processed: 283 average time/residue: 0.2533 time to fit residues: 107.3957 Evaluate side-chains 277 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 205 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 319 HIS Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.8980 chunk 168 optimal weight: 0.0770 chunk 153 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 162 optimal weight: 0.0030 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15309 Z= 0.167 Angle : 0.716 11.123 20825 Z= 0.347 Chirality : 0.043 0.228 2471 Planarity : 0.005 0.041 2520 Dihedral : 5.019 16.345 1981 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.74 % Allowed : 28.16 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 1827 helix: 0.24 (0.16), residues: 1169 sheet: -1.58 (0.54), residues: 84 loop : -3.23 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 85 HIS 0.001 0.000 HIS B 106 PHE 0.031 0.001 PHE F 299 TYR 0.026 0.001 TYR E 121 ARG 0.002 0.000 ARG G 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 229 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8217 (mttm) cc_final: 0.7864 (pttm) REVERT: A 57 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8174 (mm-30) REVERT: A 103 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.2866 (mt) REVERT: A 119 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8296 (tt) REVERT: A 128 ARG cc_start: 0.7900 (ttt-90) cc_final: 0.7444 (ttm170) REVERT: A 129 PHE cc_start: 0.8304 (m-10) cc_final: 0.8072 (m-10) REVERT: A 148 LYS cc_start: 0.8200 (tptp) cc_final: 0.7690 (mmmt) REVERT: B 57 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8113 (mm-30) REVERT: B 101 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5424 (pp) REVERT: B 103 LEU cc_start: 0.5032 (OUTLIER) cc_final: 0.2604 (mt) REVERT: B 119 LEU cc_start: 0.8652 (mt) cc_final: 0.8386 (tp) REVERT: B 262 GLN cc_start: 0.7515 (pm20) cc_final: 0.7189 (pp30) REVERT: B 272 ILE cc_start: 0.8000 (pt) cc_final: 0.7800 (tp) REVERT: C 57 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8146 (mm-30) REVERT: C 109 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6938 (t80) REVERT: C 310 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6220 (pm20) REVERT: D 103 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.2787 (mt) REVERT: D 109 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7415 (t80) REVERT: D 262 GLN cc_start: 0.7526 (pm20) cc_final: 0.7297 (pp30) REVERT: D 299 PHE cc_start: 0.6584 (t80) cc_final: 0.6152 (t80) REVERT: E 63 GLN cc_start: 0.5954 (tp40) cc_final: 0.5568 (mp10) REVERT: E 101 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5822 (pp) REVERT: E 103 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.3007 (mt) REVERT: E 109 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7206 (t80) REVERT: F 101 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5720 (pp) REVERT: F 103 LEU cc_start: 0.4901 (OUTLIER) cc_final: 0.2329 (mt) REVERT: F 109 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7247 (t80) REVERT: F 226 LEU cc_start: 0.8610 (mm) cc_final: 0.8307 (tt) REVERT: G 103 LEU cc_start: 0.4787 (OUTLIER) cc_final: 0.2210 (mt) REVERT: G 109 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.6834 (t80) REVERT: G 128 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7854 (mtp-110) REVERT: G 199 TYR cc_start: 0.7292 (m-10) cc_final: 0.6845 (m-10) REVERT: G 226 LEU cc_start: 0.8709 (mm) cc_final: 0.8241 (tt) outliers start: 80 outliers final: 55 residues processed: 290 average time/residue: 0.2510 time to fit residues: 108.6665 Evaluate side-chains 279 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 208 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 319 HIS Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.8980 chunk 172 optimal weight: 0.0170 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 0.0040 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15309 Z= 0.172 Angle : 0.728 11.378 20825 Z= 0.349 Chirality : 0.044 0.216 2471 Planarity : 0.005 0.041 2520 Dihedral : 4.930 16.291 1981 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.15 % Allowed : 28.63 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1827 helix: 0.31 (0.16), residues: 1169 sheet: -1.44 (0.54), residues: 84 loop : -3.26 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 85 HIS 0.003 0.000 HIS C 106 PHE 0.016 0.001 PHE F 273 TYR 0.026 0.001 TYR E 121 ARG 0.003 0.000 ARG A 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 222 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8247 (mttm) cc_final: 0.7891 (pttm) REVERT: A 57 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8180 (mm-30) REVERT: A 103 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.2576 (mt) REVERT: A 119 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8293 (tt) REVERT: A 128 ARG cc_start: 0.7854 (ttt-90) cc_final: 0.7314 (mtp-110) REVERT: A 129 PHE cc_start: 0.8316 (m-10) cc_final: 0.8053 (m-10) REVERT: A 148 LYS cc_start: 0.8197 (tptp) cc_final: 0.7681 (mmmt) REVERT: A 201 LYS cc_start: 0.9208 (mmtm) cc_final: 0.8978 (mmtt) REVERT: B 57 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 101 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5442 (pp) REVERT: B 103 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.2633 (mt) REVERT: B 262 GLN cc_start: 0.7509 (pm20) cc_final: 0.7189 (pp30) REVERT: C 57 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8136 (mm-30) REVERT: C 85 TRP cc_start: 0.8027 (t60) cc_final: 0.7786 (t-100) REVERT: C 109 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.6947 (t80) REVERT: C 279 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7580 (mt) REVERT: C 310 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6219 (pm20) REVERT: D 103 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.2741 (mt) REVERT: D 109 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7442 (t80) REVERT: D 262 GLN cc_start: 0.7537 (pm20) cc_final: 0.7322 (pp30) REVERT: D 299 PHE cc_start: 0.6615 (t80) cc_final: 0.6156 (t80) REVERT: E 63 GLN cc_start: 0.5881 (tp40) cc_final: 0.5551 (mp10) REVERT: E 101 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5817 (pp) REVERT: E 103 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.3027 (mt) REVERT: E 109 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7181 (t80) REVERT: E 243 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6244 (mm-30) REVERT: F 36 LYS cc_start: 0.7890 (mttm) cc_final: 0.7632 (pttt) REVERT: F 101 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5709 (pp) REVERT: F 103 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.2403 (mt) REVERT: F 109 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7403 (t80) REVERT: F 140 LYS cc_start: 0.6820 (mmtt) cc_final: 0.6605 (mmmt) REVERT: F 226 LEU cc_start: 0.8603 (mm) cc_final: 0.8306 (tt) REVERT: F 272 ILE cc_start: 0.7986 (pt) cc_final: 0.7737 (tp) REVERT: G 103 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.2220 (mt) REVERT: G 109 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.6938 (t80) REVERT: G 199 TYR cc_start: 0.7345 (m-10) cc_final: 0.6875 (m-10) REVERT: G 226 LEU cc_start: 0.8680 (mm) cc_final: 0.8241 (tt) outliers start: 70 outliers final: 49 residues processed: 279 average time/residue: 0.2594 time to fit residues: 107.3935 Evaluate side-chains 281 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 214 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 204 LYS Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 319 HIS Chi-restraints excluded: chain F residue 54 PHE Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 133 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.196893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162333 restraints weight = 29258.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.166840 restraints weight = 17247.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.169767 restraints weight = 12080.393| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15309 Z= 0.204 Angle : 0.751 11.419 20825 Z= 0.361 Chirality : 0.045 0.234 2471 Planarity : 0.005 0.041 2520 Dihedral : 5.011 23.617 1981 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.62 % Allowed : 28.57 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1827 helix: 0.32 (0.16), residues: 1169 sheet: -1.31 (0.56), residues: 84 loop : -3.26 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 85 HIS 0.002 0.001 HIS C 106 PHE 0.035 0.001 PHE F 299 TYR 0.027 0.001 TYR E 121 ARG 0.004 0.000 ARG G 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.46 seconds wall clock time: 55 minutes 40.64 seconds (3340.64 seconds total)