Starting phenix.real_space_refine on Sat Jan 20 11:38:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2t_15106/01_2024/8a2t_15106_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2t_15106/01_2024/8a2t_15106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2t_15106/01_2024/8a2t_15106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2t_15106/01_2024/8a2t_15106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2t_15106/01_2024/8a2t_15106_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2t_15106/01_2024/8a2t_15106_updated.pdb" } resolution = 2.24 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= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9145 2.51 5 N 2445 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15046 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Time building chain proxies: 8.54, per 1000 atoms: 0.57 Number of scatterers: 15046 At special positions: 0 Unit cell: (96.605, 91.045, 193.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 O 3341 8.00 N 2445 7.00 C 9145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.87 Conformation dependent library (CDL) restraints added in 2.8 seconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 20 sheets defined 44.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.797A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.677A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.984A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.525A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.752A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 370 Proline residue: C 367 - end of helix removed outlier: 5.003A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.796A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.676A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.984A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.525A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.751A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 370 Proline residue: A 367 - end of helix removed outlier: 5.003A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.797A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.676A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.984A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.525A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.752A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 370 Proline residue: B 367 - end of helix removed outlier: 5.003A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.797A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.676A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.985A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.525A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.752A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 370 Proline residue: D 367 - end of helix removed outlier: 5.003A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.797A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.677A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.984A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.525A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.751A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 359 through 370 Proline residue: E 367 - end of helix removed outlier: 5.003A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.580A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.284A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.579A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.284A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.579A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.284A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.580A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.284A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.580A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.284A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 525 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 6.32 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: 4701 1.34 - 1.46: 2868 1.46 - 1.57: 7046 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14805 Sorted by residual: bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.53e+00 ... (remaining 14800 not shown) Histogram of bond angle deviations from ideal: 99.88 - 107.18: 630 107.18 - 114.47: 8632 114.47 - 121.77: 7599 121.77 - 129.06: 3134 129.06 - 136.36: 95 Bond angle restraints: 20090 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.71 110.30 3.41 9.50e-01 1.11e+00 1.29e+01 angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.71 110.31 3.40 9.50e-01 1.11e+00 1.28e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.71 110.36 3.35 9.50e-01 1.11e+00 1.24e+01 angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 113.71 110.36 3.35 9.50e-01 1.11e+00 1.24e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.71 110.37 3.34 9.50e-01 1.11e+00 1.24e+01 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.63: 8790 33.63 - 67.27: 80 67.27 - 100.90: 30 100.90 - 134.54: 5 134.54 - 168.17: 5 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.18 -168.17 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.16 -168.16 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.14 -168.14 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1239 0.031 - 0.062: 696 0.062 - 0.094: 176 0.094 - 0.125: 113 0.125 - 0.156: 6 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO C 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO E 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO A 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.014 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 133 2.48 - 3.09: 10522 3.09 - 3.69: 24390 3.69 - 4.30: 39991 4.30 - 4.90: 61137 Nonbonded interactions: 136173 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 522 " model vdw 1.880 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 528 " model vdw 1.891 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 544 " model vdw 1.892 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 536 " model vdw 1.925 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 545 " model vdw 1.928 2.170 ... (remaining 136168 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' } 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 individual isotropic 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: 3.110 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: 12.220 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 42.090 Find NCS groups from input model: 0.920 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:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14805 Z= 0.254 Angle : 0.564 7.282 20090 Z= 0.286 Chirality : 0.044 0.156 2230 Planarity : 0.004 0.026 2565 Dihedral : 13.196 168.175 5510 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % 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: -1.62 (0.19), residues: 1795 helix: -2.37 (0.14), residues: 785 sheet: -1.01 (0.25), residues: 305 loop : 0.95 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS B 161 PHE 0.007 0.001 PHE E 262 TYR 0.009 0.001 TYR E 143 ARG 0.003 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 246 time to evaluate : 1.883 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7078 (mp10) cc_final: 0.6659 (mp10) REVERT: B 41 GLN cc_start: 0.6963 (mp10) cc_final: 0.6663 (mp10) REVERT: B 72 GLU cc_start: 0.7419 (tp30) cc_final: 0.7020 (tp30) REVERT: B 121 GLN cc_start: 0.8126 (tt0) cc_final: 0.7901 (tt0) REVERT: B 123 MET cc_start: 0.8970 (mmt) cc_final: 0.8715 (mmp) REVERT: D 25 ASP cc_start: 0.7743 (p0) cc_final: 0.7349 (m-30) REVERT: D 41 GLN cc_start: 0.6559 (mp10) cc_final: 0.6338 (mp10) REVERT: E 41 GLN cc_start: 0.6894 (mp10) cc_final: 0.6554 (mp10) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 1.5975 time to fit residues: 432.6275 Evaluate side-chains 188 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 0.0570 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN A 225 ASN A 246 GLN A 354 GLN B 354 GLN D 40 HIS D 246 GLN D 353 GLN E 40 HIS E 353 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14805 Z= 0.154 Angle : 0.542 6.839 20090 Z= 0.257 Chirality : 0.043 0.152 2230 Planarity : 0.004 0.034 2565 Dihedral : 11.888 179.147 2057 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.16 % Allowed : 7.81 % Favored : 91.03 % 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: 0.07 (0.20), residues: 1795 helix: -0.66 (0.17), residues: 790 sheet: -0.42 (0.24), residues: 345 loop : 1.71 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS D 161 PHE 0.010 0.001 PHE D 255 TYR 0.012 0.001 TYR E 143 ARG 0.003 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 1.662 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7133 (mp10) cc_final: 0.6711 (mp10) REVERT: C 68 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8403 (mttp) REVERT: C 328 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8169 (tttt) REVERT: B 41 GLN cc_start: 0.7023 (mp10) cc_final: 0.6672 (mp10) REVERT: B 57 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6745 (pt0) REVERT: B 72 GLU cc_start: 0.7424 (tp30) cc_final: 0.7055 (tp30) REVERT: B 354 GLN cc_start: 0.7951 (pt0) cc_final: 0.7718 (pm20) REVERT: D 25 ASP cc_start: 0.7755 (p0) cc_final: 0.7436 (m-30) REVERT: D 41 GLN cc_start: 0.6620 (mp10) cc_final: 0.6351 (mp10) REVERT: D 95 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7536 (mtp180) REVERT: E 41 GLN cc_start: 0.7012 (mp10) cc_final: 0.6589 (mp10) outliers start: 18 outliers final: 4 residues processed: 202 average time/residue: 1.6225 time to fit residues: 354.3985 Evaluate side-chains 189 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 353 GLN A 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14805 Z= 0.434 Angle : 0.681 9.256 20090 Z= 0.337 Chirality : 0.051 0.194 2230 Planarity : 0.005 0.048 2565 Dihedral : 12.339 174.428 2055 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.68 % Allowed : 8.19 % Favored : 90.13 % 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: 0.44 (0.20), residues: 1795 helix: -0.19 (0.18), residues: 790 sheet: -0.44 (0.27), residues: 315 loop : 1.70 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 340 HIS 0.005 0.001 HIS B 173 PHE 0.021 0.002 PHE D 262 TYR 0.015 0.002 TYR E 143 ARG 0.005 0.001 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7118 (mp10) cc_final: 0.6726 (mp10) REVERT: C 121 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: C 125 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: C 328 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8143 (tttt) REVERT: A 64 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8696 (pp) REVERT: B 41 GLN cc_start: 0.7060 (mp10) cc_final: 0.6784 (mp10) REVERT: B 72 GLU cc_start: 0.7443 (tp30) cc_final: 0.7152 (tp30) REVERT: D 25 ASP cc_start: 0.7864 (p0) cc_final: 0.7485 (m-30) REVERT: D 95 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7555 (mtp180) REVERT: E 41 GLN cc_start: 0.6920 (mp10) cc_final: 0.6523 (mp10) REVERT: E 314 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7838 (tt0) outliers start: 26 outliers final: 6 residues processed: 188 average time/residue: 1.6058 time to fit residues: 326.9155 Evaluate side-chains 178 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14805 Z= 0.172 Angle : 0.548 6.909 20090 Z= 0.260 Chirality : 0.044 0.154 2230 Planarity : 0.003 0.041 2565 Dihedral : 11.832 172.024 2055 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.35 % Allowed : 9.29 % Favored : 89.35 % 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: 0.86 (0.21), residues: 1795 helix: 0.17 (0.19), residues: 790 sheet: -0.15 (0.25), residues: 345 loop : 1.93 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.003 0.001 HIS E 87 PHE 0.011 0.001 PHE D 262 TYR 0.008 0.001 TYR E 143 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 1.848 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7118 (mp10) cc_final: 0.6751 (mp10) REVERT: C 64 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8468 (pp) REVERT: C 125 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: C 328 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8166 (tttt) REVERT: A 64 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8639 (pp) REVERT: B 41 GLN cc_start: 0.7019 (mp10) cc_final: 0.6766 (mp10) REVERT: D 25 ASP cc_start: 0.7796 (p0) cc_final: 0.7485 (m-30) REVERT: D 95 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7561 (mtp180) REVERT: E 41 GLN cc_start: 0.6926 (mp10) cc_final: 0.6451 (mp10) outliers start: 21 outliers final: 6 residues processed: 192 average time/residue: 1.5772 time to fit residues: 328.3735 Evaluate side-chains 183 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14805 Z= 0.322 Angle : 0.623 8.180 20090 Z= 0.303 Chirality : 0.048 0.177 2230 Planarity : 0.004 0.041 2565 Dihedral : 12.154 179.637 2055 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.74 % Allowed : 9.16 % Favored : 89.10 % 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: 0.80 (0.20), residues: 1795 helix: 0.18 (0.19), residues: 790 sheet: -0.36 (0.27), residues: 315 loop : 1.83 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.005 0.001 HIS A 161 PHE 0.017 0.002 PHE D 262 TYR 0.011 0.001 TYR E 143 ARG 0.003 0.001 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.857 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7113 (mp10) cc_final: 0.6751 (mp10) REVERT: C 64 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8544 (pp) REVERT: C 121 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: C 125 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: C 328 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8166 (tttt) REVERT: A 64 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8695 (pp) REVERT: A 326 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8024 (mmtt) REVERT: B 41 GLN cc_start: 0.6982 (mp10) cc_final: 0.6687 (mp10) REVERT: D 25 ASP cc_start: 0.7822 (p0) cc_final: 0.7484 (m-30) REVERT: D 95 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7562 (mtp180) REVERT: E 41 GLN cc_start: 0.6889 (mp10) cc_final: 0.6389 (mp10) REVERT: E 125 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6846 (mp0) outliers start: 27 outliers final: 10 residues processed: 189 average time/residue: 1.7377 time to fit residues: 355.2746 Evaluate side-chains 185 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 0.0970 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14805 Z= 0.287 Angle : 0.605 7.829 20090 Z= 0.293 Chirality : 0.047 0.172 2230 Planarity : 0.004 0.041 2565 Dihedral : 12.103 179.507 2055 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.42 % Allowed : 9.68 % Favored : 88.90 % 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: 0.86 (0.20), residues: 1795 helix: 0.24 (0.19), residues: 790 sheet: -0.37 (0.27), residues: 315 loop : 1.88 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 340 HIS 0.004 0.001 HIS A 161 PHE 0.015 0.002 PHE D 262 TYR 0.010 0.001 TYR E 143 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 1.779 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7111 (mp10) cc_final: 0.6762 (mp10) REVERT: C 64 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8524 (pp) REVERT: C 121 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: C 125 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: C 328 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8169 (tttt) REVERT: A 44 MET cc_start: 0.7995 (mtp) cc_final: 0.7786 (mtp) REVERT: A 64 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8692 (pp) REVERT: A 326 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8007 (mmtt) REVERT: B 41 GLN cc_start: 0.6973 (mp10) cc_final: 0.6688 (mp10) REVERT: D 25 ASP cc_start: 0.7827 (p0) cc_final: 0.7528 (m-30) REVERT: D 64 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8490 (pp) REVERT: D 95 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7592 (mtp180) REVERT: E 41 GLN cc_start: 0.6886 (mp10) cc_final: 0.6374 (mp10) outliers start: 22 outliers final: 10 residues processed: 192 average time/residue: 1.6060 time to fit residues: 334.2885 Evaluate side-chains 190 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 173 optimal weight: 0.0970 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14805 Z= 0.177 Angle : 0.550 6.928 20090 Z= 0.261 Chirality : 0.044 0.154 2230 Planarity : 0.003 0.040 2565 Dihedral : 11.731 171.546 2055 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.16 % Allowed : 9.94 % Favored : 88.90 % 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: 1.08 (0.21), residues: 1795 helix: 0.39 (0.19), residues: 790 sheet: -0.12 (0.26), residues: 345 loop : 2.06 (0.27), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 79 HIS 0.004 0.001 HIS A 161 PHE 0.010 0.001 PHE D 262 TYR 0.007 0.001 TYR B 143 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7143 (mp10) cc_final: 0.6808 (mp10) REVERT: C 64 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8473 (pp) REVERT: C 121 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: C 328 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8163 (tttt) REVERT: A 64 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8646 (pp) REVERT: B 41 GLN cc_start: 0.6958 (mp10) cc_final: 0.6708 (mp10) REVERT: D 25 ASP cc_start: 0.7784 (p0) cc_final: 0.7496 (m-30) REVERT: D 64 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8434 (pp) REVERT: D 95 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7589 (mtp180) REVERT: E 41 GLN cc_start: 0.6877 (mp10) cc_final: 0.6386 (mp10) outliers start: 18 outliers final: 9 residues processed: 190 average time/residue: 1.6057 time to fit residues: 331.3558 Evaluate side-chains 185 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14805 Z= 0.329 Angle : 0.628 8.230 20090 Z= 0.305 Chirality : 0.048 0.177 2230 Planarity : 0.004 0.040 2565 Dihedral : 12.127 179.246 2055 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.42 % Allowed : 10.06 % Favored : 88.52 % 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: 0.91 (0.20), residues: 1795 helix: 0.28 (0.19), residues: 790 sheet: -0.35 (0.27), residues: 315 loop : 1.91 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.005 0.001 HIS A 161 PHE 0.017 0.002 PHE D 262 TYR 0.010 0.001 TYR D 188 ARG 0.004 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 169 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7107 (mp10) cc_final: 0.6764 (mp10) REVERT: C 64 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8557 (pp) REVERT: C 121 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: C 125 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: C 328 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8170 (tttt) REVERT: A 64 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8704 (pp) REVERT: A 326 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8008 (mmtt) REVERT: A 359 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7459 (tmtt) REVERT: D 25 ASP cc_start: 0.7808 (p0) cc_final: 0.7509 (m-30) REVERT: D 64 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8490 (pp) REVERT: D 95 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7579 (mtp180) REVERT: E 41 GLN cc_start: 0.6851 (mp10) cc_final: 0.6352 (mp10) REVERT: E 314 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7988 (tt0) outliers start: 22 outliers final: 12 residues processed: 184 average time/residue: 1.6131 time to fit residues: 322.2816 Evaluate side-chains 192 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14805 Z= 0.314 Angle : 0.622 8.048 20090 Z= 0.302 Chirality : 0.047 0.178 2230 Planarity : 0.004 0.040 2565 Dihedral : 12.138 179.598 2055 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.42 % Allowed : 10.06 % Favored : 88.52 % 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: 0.89 (0.20), residues: 1795 helix: 0.27 (0.19), residues: 790 sheet: -0.38 (0.27), residues: 315 loop : 1.90 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.005 0.001 HIS A 161 PHE 0.016 0.002 PHE D 262 TYR 0.011 0.001 TYR D 188 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7095 (mp10) cc_final: 0.6756 (mp10) REVERT: C 64 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8564 (pp) REVERT: C 121 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: C 125 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: C 328 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8168 (tttt) REVERT: A 64 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8701 (pp) REVERT: A 326 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8000 (mmtt) REVERT: A 359 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7516 (tmtt) REVERT: B 41 GLN cc_start: 0.6986 (mp10) cc_final: 0.6717 (mp10) REVERT: D 25 ASP cc_start: 0.7821 (p0) cc_final: 0.7518 (m-30) REVERT: D 64 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8476 (pp) REVERT: D 95 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7583 (mtp180) REVERT: E 41 GLN cc_start: 0.6845 (mp10) cc_final: 0.6343 (mp10) REVERT: E 314 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8015 (tt0) outliers start: 22 outliers final: 11 residues processed: 186 average time/residue: 1.6797 time to fit residues: 338.4051 Evaluate side-chains 190 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 4.9990 chunk 104 optimal weight: 0.0470 chunk 81 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14805 Z= 0.267 Angle : 0.599 7.708 20090 Z= 0.289 Chirality : 0.046 0.171 2230 Planarity : 0.004 0.041 2565 Dihedral : 12.056 178.829 2055 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.29 % Allowed : 10.19 % Favored : 88.52 % 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: 0.95 (0.20), residues: 1795 helix: 0.33 (0.19), residues: 790 sheet: -0.35 (0.27), residues: 315 loop : 1.92 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 340 HIS 0.004 0.001 HIS A 161 PHE 0.015 0.002 PHE D 262 TYR 0.009 0.001 TYR D 188 ARG 0.003 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7112 (mp10) cc_final: 0.6770 (mp10) REVERT: C 64 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8521 (pp) REVERT: C 121 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: C 125 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: C 328 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8168 (tttt) REVERT: A 44 MET cc_start: 0.7965 (mtp) cc_final: 0.7740 (mtt) REVERT: A 64 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 359 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7495 (tmtt) REVERT: B 41 GLN cc_start: 0.6946 (mp10) cc_final: 0.6686 (mp10) REVERT: D 25 ASP cc_start: 0.7813 (p0) cc_final: 0.7521 (m-30) REVERT: D 64 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8469 (pp) REVERT: D 95 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7587 (mtp180) REVERT: E 41 GLN cc_start: 0.6858 (mp10) cc_final: 0.6355 (mp10) REVERT: E 314 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8022 (tt0) outliers start: 20 outliers final: 11 residues processed: 189 average time/residue: 1.6038 time to fit residues: 328.7486 Evaluate side-chains 194 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.093577 restraints weight = 15669.254| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.21 r_work: 0.2953 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14805 Z= 0.285 Angle : 0.610 7.836 20090 Z= 0.295 Chirality : 0.047 0.175 2230 Planarity : 0.004 0.040 2565 Dihedral : 12.094 179.060 2055 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.48 % Allowed : 9.87 % Favored : 88.65 % 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: 0.93 (0.20), residues: 1795 helix: 0.32 (0.19), residues: 790 sheet: -0.37 (0.27), residues: 315 loop : 1.91 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 340 HIS 0.005 0.001 HIS A 161 PHE 0.015 0.002 PHE D 262 TYR 0.010 0.001 TYR D 188 ARG 0.003 0.000 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6231.02 seconds wall clock time: 111 minutes 22.34 seconds (6682.34 seconds total)