Starting phenix.real_space_refine on Sun Dec 10 16:02:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/12_2023/6m67_30115.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/12_2023/6m67_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_30115/12_2023/6m67_30115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/12_2023/6m67_30115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/12_2023/6m67_30115.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/12_2023/6m67_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-1.21rc1-5172/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: 8.14, per 1000 atoms: 0.54 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: 5.63 Conformation dependent library (CDL) restraints added in 2.9 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: 1.53 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: 3.89 Time building geometry restraints manager: 6.11 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: 1.040 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: 4.160 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 39.680 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.050 ------------------------------------------------------------------------------- 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 : 1.557 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 outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2597 time to fit residues: 148.9476 Evaluate side-chains 231 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3580 ------------------------------------------------------------------------------- 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: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.6367 moved from start: 0.2465 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= 0.193 Angle : 0.779 9.733 20825 Z= 0.393 Chirality : 0.045 0.213 2471 Planarity : 0.007 0.056 2520 Dihedral : 6.384 22.899 1981 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 1.66 % Allowed : 18.67 % Favored : 79.67 % 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: -3.50 (0.18), residues: 1827 helix: -1.52 (0.14), residues: 1113 sheet: -2.74 (0.42), residues: 84 loop : -3.59 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 127 HIS 0.003 0.001 HIS F 106 PHE 0.031 0.002 PHE D 299 TYR 0.027 0.002 TYR E 121 ARG 0.003 0.000 ARG A 128 *********************** 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 311 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 283 time to evaluate : 1.752 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 outliers start: 28 outliers final: 6 residues processed: 305 average time/residue: 0.2421 time to fit residues: 113.1399 Evaluate side-chains 231 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1396 time to fit residues: 3.9755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 76 GLN A 90 GLN ** B 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 76 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15309 Z= 0.222 Angle : 0.786 10.496 20825 Z= 0.387 Chirality : 0.046 0.221 2471 Planarity : 0.006 0.050 2520 Dihedral : 6.003 21.283 1981 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.85 % Allowed : 22.35 % Favored : 74.81 % 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: -2.57 (0.19), residues: 1827 helix: -0.70 (0.15), residues: 1113 sheet: -1.96 (0.47), residues: 84 loop : -3.47 (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 0.025 0.002 PHE G 126 TYR 0.029 0.002 TYR E 121 ARG 0.004 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 282 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 1.800 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 outliers start: 48 outliers final: 32 residues processed: 265 average time/residue: 0.2470 time to fit residues: 99.6607 Evaluate side-chains 239 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1363 time to fit residues: 10.4236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15309 Z= 0.181 Angle : 0.735 10.169 20825 Z= 0.361 Chirality : 0.044 0.219 2471 Planarity : 0.005 0.047 2520 Dihedral : 5.622 19.233 1981 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.61 % Allowed : 24.54 % Favored : 72.85 % 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: -1.99 (0.20), residues: 1827 helix: -0.34 (0.16), residues: 1155 sheet: -1.93 (0.47), residues: 84 loop : -3.17 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 85 HIS 0.002 0.001 HIS F 106 PHE 0.018 0.001 PHE G 126 TYR 0.028 0.002 TYR C 121 ARG 0.002 0.000 ARG A 254 *********************** 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 299 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 255 time to evaluate : 1.776 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 outliers start: 44 outliers final: 21 residues processed: 280 average time/residue: 0.2467 time to fit residues: 104.7692 Evaluate side-chains 230 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1398 time to fit residues: 7.9262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 130 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 chunk 150 optimal weight: 0.1980 chunk 121 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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** A 274 GLN C 56 GLN C 274 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 F 90 GLN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 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 0.040 15309 Z= 0.163 Angle : 0.744 10.125 20825 Z= 0.359 Chirality : 0.044 0.217 2471 Planarity : 0.005 0.046 2520 Dihedral : 5.286 22.326 1981 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.25 % Allowed : 27.03 % Favored : 70.72 % 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: -1.80 (0.20), residues: 1827 helix: -0.12 (0.16), residues: 1169 sheet: -2.29 (0.46), residues: 91 loop : -3.24 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 85 HIS 0.004 0.001 HIS F 106 PHE 0.024 0.001 PHE F 299 TYR 0.029 0.002 TYR C 121 ARG 0.001 0.000 ARG C 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 290 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 252 time to evaluate : 1.607 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 outliers start: 38 outliers final: 12 residues processed: 276 average time/residue: 0.2618 time to fit residues: 106.4506 Evaluate side-chains 220 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1377 time to fit residues: 5.4658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 0.3980 chunk 146 optimal weight: 0.0070 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN F 90 GLN F 274 GLN G 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15309 Z= 0.180 Angle : 0.747 10.638 20825 Z= 0.363 Chirality : 0.045 0.239 2471 Planarity : 0.005 0.043 2520 Dihedral : 5.225 23.826 1981 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.61 % Allowed : 27.80 % Favored : 69.59 % 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: -1.65 (0.20), residues: 1827 helix: 0.00 (0.16), residues: 1169 sheet: -1.99 (0.49), residues: 91 loop : -3.24 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 85 HIS 0.003 0.001 HIS F 106 PHE 0.018 0.001 PHE B 320 TYR 0.030 0.002 TYR C 121 ARG 0.002 0.000 ARG A 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 270 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 1.820 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 outliers start: 44 outliers final: 20 residues processed: 257 average time/residue: 0.2739 time to fit residues: 103.7956 Evaluate side-chains 216 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1475 time to fit residues: 7.6506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 0.0010 chunk 128 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 148 optimal weight: 0.0370 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 overall best weight: 0.3664 ------------------------------------------------------------------------------- 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** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15309 Z= 0.162 Angle : 0.741 10.870 20825 Z= 0.355 Chirality : 0.044 0.209 2471 Planarity : 0.005 0.042 2520 Dihedral : 4.980 19.565 1981 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.54 % Allowed : 28.93 % Favored : 69.53 % 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: -1.42 (0.20), residues: 1827 helix: 0.18 (0.16), residues: 1169 sheet: -1.51 (0.50), residues: 84 loop : -3.22 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 85 HIS 0.002 0.000 HIS D 106 PHE 0.031 0.001 PHE F 299 TYR 0.032 0.001 TYR C 121 ARG 0.002 0.000 ARG A 128 *********************** 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 273 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 247 time to evaluate : 1.706 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 outliers start: 26 outliers final: 12 residues processed: 258 average time/residue: 0.2774 time to fit residues: 104.5012 Evaluate side-chains 225 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1420 time to fit residues: 5.3857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.0040 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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** ** B 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** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15309 Z= 0.176 Angle : 0.764 10.530 20825 Z= 0.367 Chirality : 0.045 0.260 2471 Planarity : 0.005 0.042 2520 Dihedral : 5.066 24.635 1981 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 1.24 % Allowed : 29.82 % Favored : 68.94 % 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: -1.36 (0.20), residues: 1827 helix: 0.27 (0.16), residues: 1162 sheet: -0.94 (0.56), residues: 70 loop : -3.31 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 85 HIS 0.002 0.001 HIS F 106 PHE 0.023 0.001 PHE E 108 TYR 0.031 0.001 TYR C 121 ARG 0.002 0.000 ARG C 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 259 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 238 time to evaluate : 1.824 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 outliers start: 21 outliers final: 14 residues processed: 252 average time/residue: 0.2872 time to fit residues: 104.4336 Evaluate side-chains 221 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 207 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1540 time to fit residues: 6.1108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 0.0040 chunk 50 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 162 optimal weight: 0.1980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15309 Z= 0.173 Angle : 0.765 10.384 20825 Z= 0.366 Chirality : 0.044 0.168 2471 Planarity : 0.005 0.043 2520 Dihedral : 4.980 19.232 1981 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.77 % Allowed : 30.17 % Favored : 69.06 % 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: -1.28 (0.20), residues: 1827 helix: 0.29 (0.16), residues: 1176 sheet: -0.83 (0.59), residues: 70 loop : -3.28 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 127 HIS 0.002 0.000 HIS F 106 PHE 0.032 0.001 PHE G 299 TYR 0.032 0.001 TYR C 121 ARG 0.004 0.000 ARG A 128 *********************** 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 249 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 236 time to evaluate : 1.840 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 outliers start: 13 outliers final: 7 residues processed: 242 average time/residue: 0.2883 time to fit residues: 100.6666 Evaluate side-chains 227 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1313 time to fit residues: 3.8381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9980 chunk 172 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** 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** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15309 Z= 0.185 Angle : 0.783 10.506 20825 Z= 0.373 Chirality : 0.045 0.210 2471 Planarity : 0.005 0.042 2520 Dihedral : 4.953 18.970 1981 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.53 % Allowed : 30.41 % Favored : 69.06 % 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: -1.25 (0.20), residues: 1827 helix: 0.32 (0.16), residues: 1176 sheet: -0.66 (0.62), residues: 70 loop : -3.30 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 85 HIS 0.002 0.001 HIS F 106 PHE 0.022 0.001 PHE F 244 TYR 0.031 0.001 TYR C 121 ARG 0.003 0.000 ARG A 128 ********************** 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 239 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 230 time to evaluate : 1.711 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 outliers start: 9 outliers final: 4 residues processed: 234 average time/residue: 0.2939 time to fit residues: 99.3079 Evaluate side-chains 208 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1512 time to fit residues: 3.5830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 0.0670 chunk 18 optimal weight: 0.0770 chunk 26 optimal weight: 0.7980 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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** ** B 76 GLN ** 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** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** 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 = 0.4540 r_free = 0.4540 target = 0.201484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.166979 restraints weight = 29270.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.171575 restraints weight = 17395.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.174419 restraints weight = 12227.369| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.5204 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= 0.186 Angle : 0.806 12.023 20825 Z= 0.381 Chirality : 0.046 0.195 2471 Planarity : 0.005 0.043 2520 Dihedral : 4.985 20.381 1981 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.41 % Allowed : 31.00 % Favored : 68.58 % 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: -1.24 (0.20), residues: 1827 helix: 0.31 (0.16), residues: 1183 sheet: -0.66 (0.59), residues: 70 loop : -3.30 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.002 0.000 HIS F 106 PHE 0.034 0.001 PHE G 299 TYR 0.032 0.001 TYR C 121 ARG 0.003 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.36 seconds wall clock time: 55 minutes 45.82 seconds (3345.82 seconds total)