Starting phenix.real_space_refine on Sat Mar 16 16:40:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2z_15109/03_2024/8a2z_15109_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2z_15109/03_2024/8a2z_15109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2z_15109/03_2024/8a2z_15109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2z_15109/03_2024/8a2z_15109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2z_15109/03_2024/8a2z_15109_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2z_15109/03_2024/8a2z_15109_updated.pdb" } resolution = 2.15 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 Ca 5 9.91 5 P 10 5.49 5 S 100 5.16 5 C 9145 2.51 5 N 2445 2.21 5 O 3355 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 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 "C GLU 270": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" 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 "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" 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 "B GLU 270": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" 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 "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" 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" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15060 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: {' CA': 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: {' CA': 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: {' CA': 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: {' CA': 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: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Time building chain proxies: 7.75, per 1000 atoms: 0.51 Number of scatterers: 15060 At special positions: 0 Unit cell: (95.215, 91.74, 191.82, 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) Ca 5 19.99 S 100 16.00 P 10 15.00 O 3355 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: 5.43 Conformation dependent library (CDL) restraints added in 2.4 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, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 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: 3.736A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.542A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.706A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.470A 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: 3.570A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.949A 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: 5.330A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 4.038A 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: 4.874A 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: 3.736A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.543A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.707A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.469A 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: 3.571A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.949A 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: 5.330A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 4.038A 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: 4.873A 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: 3.736A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.543A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.707A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.469A 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: 3.572A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.949A 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: 5.330A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 4.038A 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: 4.873A 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: 3.735A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.544A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.707A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.469A 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: 3.572A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.950A 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: 5.330A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 4.038A 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: 4.873A 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: 3.736A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.543A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.706A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.469A 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: 3.572A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.950A 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: 5.331A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 4.037A 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: 4.873A 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: 6.595A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.259A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.214A 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: 6.595A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= G, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.258A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.214A 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: 6.595A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= K, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.258A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.214A 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: 6.595A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.258A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.214A 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: 6.596A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 52 through 54 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.258A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.214A 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. 1290 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: 4.80 Time building geometry restraints manager: 5.95 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: 4705 1.34 - 1.46: 3130 1.46 - 1.58: 6780 1.58 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14805 Sorted by residual: 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 7.54e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 ... (remaining 14800 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.80: 575 106.80 - 114.16: 8542 114.16 - 121.52: 7525 121.52 - 128.88: 3353 128.88 - 136.25: 95 Bond angle restraints: 20090 Sorted by residual: angle pdb=" NE ARG A 39 " pdb=" CZ ARG A 39 " pdb=" NH2 ARG A 39 " ideal model delta sigma weight residual 119.20 121.54 -2.34 9.00e-01 1.23e+00 6.78e+00 angle pdb=" NE ARG D 95 " pdb=" CZ ARG D 95 " pdb=" NH2 ARG D 95 " ideal model delta sigma weight residual 119.20 121.52 -2.32 9.00e-01 1.23e+00 6.66e+00 angle pdb=" NE ARG D 39 " pdb=" CZ ARG D 39 " pdb=" NH2 ARG D 39 " ideal model delta sigma weight residual 119.20 121.52 -2.32 9.00e-01 1.23e+00 6.62e+00 angle pdb=" NE ARG E 256 " pdb=" CZ ARG E 256 " pdb=" NH2 ARG E 256 " ideal model delta sigma weight residual 119.20 121.51 -2.31 9.00e-01 1.23e+00 6.58e+00 angle pdb=" NE ARG A 37 " pdb=" CZ ARG A 37 " pdb=" NH2 ARG A 37 " ideal model delta sigma weight residual 119.20 121.51 -2.31 9.00e-01 1.23e+00 6.58e+00 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 8665 23.67 - 47.34: 195 47.34 - 71.00: 15 71.00 - 94.67: 30 94.67 - 118.34: 5 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.34 118.34 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.30 118.29 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.29 118.29 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1292 0.031 - 0.063: 625 0.063 - 0.094: 198 0.094 - 0.126: 109 0.126 - 0.157: 6 Chirality restraints: 2230 Sorted by residual: 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 -2.67 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C3' ADP D 401 " pdb=" C2' ADP D 401 " pdb=" C4' ADP D 401 " pdb=" O3' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO C 243 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO D 243 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 243 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.014 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1063 2.73 - 3.27: 15529 3.27 - 3.82: 28005 3.82 - 4.36: 35875 4.36 - 4.90: 56736 Nonbonded interactions: 137208 Sorted by model distance: nonbonded pdb="CA CA B 402 " pdb=" O HOH B 578 " model vdw 2.190 2.510 nonbonded pdb="CA CA A 402 " pdb=" O HOH A 556 " model vdw 2.206 2.510 nonbonded pdb=" O2B ADP B 401 " pdb="CA CA B 402 " model vdw 2.217 2.510 nonbonded pdb=" O2B ADP E 401 " pdb="CA CA E 402 " model vdw 2.217 2.510 nonbonded pdb=" O2B ADP A 401 " pdb="CA CA A 402 " model vdw 2.217 2.510 ... (remaining 137203 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: 2.500 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: 12.280 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 40.840 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 0.055 14805 Z= 0.251 Angle : 0.582 7.015 20090 Z= 0.292 Chirality : 0.043 0.157 2230 Planarity : 0.004 0.033 2565 Dihedral : 11.913 118.341 5510 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.06 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -1.13 (0.19), residues: 1795 helix: -1.95 (0.15), residues: 785 sheet: -0.73 (0.27), residues: 320 loop : 1.21 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 340 HIS 0.003 0.001 HIS E 161 PHE 0.008 0.001 PHE E 262 TYR 0.009 0.001 TYR D 143 ARG 0.003 0.001 ARG B 210 *********************** 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 258 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.572 Fit side-chains REVERT: B 225 ASN cc_start: 0.7901 (m-40) cc_final: 0.7690 (m110) REVERT: B 227 MET cc_start: 0.8770 (mmm) cc_final: 0.8533 (mmm) REVERT: B 286 ASP cc_start: 0.7554 (m-30) cc_final: 0.7347 (m-30) REVERT: D 92 ASN cc_start: 0.8523 (m-40) cc_final: 0.8307 (m110) REVERT: D 128 ASN cc_start: 0.8408 (m-40) cc_final: 0.8200 (m110) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 1.6062 time to fit residues: 447.8612 Evaluate side-chains 185 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 225 ASN A 246 GLN A 353 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 88 HIS B 161 HIS B 360 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS E 246 GLN E 353 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14805 Z= 0.292 Angle : 0.633 7.517 20090 Z= 0.312 Chirality : 0.047 0.175 2230 Planarity : 0.004 0.040 2565 Dihedral : 9.397 126.920 2055 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.23 % Allowed : 8.32 % Favored : 90.45 % 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: 0.19 (0.20), residues: 1795 helix: -0.61 (0.17), residues: 790 sheet: -0.50 (0.26), residues: 320 loop : 1.84 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS E 161 PHE 0.012 0.002 PHE B 262 TYR 0.013 0.001 TYR A 143 ARG 0.004 0.001 ARG E 62 *********************** 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 213 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.838 Fit side-chains REVERT: D 92 ASN cc_start: 0.8505 (m-40) cc_final: 0.8302 (m110) REVERT: E 95 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7416 (mtp-110) outliers start: 19 outliers final: 9 residues processed: 204 average time/residue: 1.5195 time to fit residues: 336.2965 Evaluate side-chains 191 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 0.0070 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN A 353 GLN B 225 ASN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14805 Z= 0.159 Angle : 0.554 6.857 20090 Z= 0.265 Chirality : 0.043 0.164 2230 Planarity : 0.003 0.033 2565 Dihedral : 8.929 123.240 2055 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.42 % Allowed : 8.39 % Favored : 90.19 % 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: 0.67 (0.20), residues: 1795 helix: -0.17 (0.18), residues: 790 sheet: -0.30 (0.25), residues: 350 loop : 2.18 (0.27), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE B 255 TYR 0.008 0.001 TYR A 143 ARG 0.002 0.000 ARG B 95 *********************** 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 203 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.697 Fit side-chains REVERT: B 355 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7282 (mtm) REVERT: D 95 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7252 (mpp-170) REVERT: E 95 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7390 (mtp-110) REVERT: E 360 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7368 (mp-120) outliers start: 22 outliers final: 8 residues processed: 194 average time/residue: 1.5399 time to fit residues: 324.0363 Evaluate side-chains 192 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 164 optimal weight: 0.5980 chunk 173 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 360 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN D 88 HIS D 92 ASN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14805 Z= 0.234 Angle : 0.596 7.365 20090 Z= 0.288 Chirality : 0.045 0.174 2230 Planarity : 0.004 0.033 2565 Dihedral : 9.190 125.984 2055 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.61 % Allowed : 8.90 % Favored : 89.48 % 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: 0.77 (0.21), residues: 1795 helix: -0.03 (0.18), residues: 790 sheet: -0.34 (0.27), residues: 320 loop : 2.10 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG E 62 *********************** 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 208 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.583 Fit side-chains REVERT: B 355 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7293 (mtm) REVERT: D 95 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7235 (mpp-170) REVERT: E 95 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7359 (mtp-110) REVERT: E 360 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7387 (mp-120) outliers start: 25 outliers final: 14 residues processed: 197 average time/residue: 1.4824 time to fit residues: 317.3370 Evaluate side-chains 195 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN 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: 0.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN D 246 GLN E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14805 Z= 0.379 Angle : 0.675 8.163 20090 Z= 0.333 Chirality : 0.050 0.187 2230 Planarity : 0.004 0.046 2565 Dihedral : 9.705 131.027 2055 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.94 % Allowed : 9.10 % Favored : 88.97 % 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: 0.73 (0.20), residues: 1795 helix: -0.04 (0.18), residues: 790 sheet: -0.37 (0.27), residues: 320 loop : 2.03 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 340 HIS 0.004 0.001 HIS D 161 PHE 0.014 0.002 PHE B 262 TYR 0.010 0.001 TYR A 143 ARG 0.005 0.001 ARG E 62 *********************** 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 208 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 1.628 Fit side-chains REVERT: B 355 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7311 (mtm) REVERT: D 95 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7248 (mpp-170) REVERT: D 354 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7463 (pp30) REVERT: E 44 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7767 (mmm) REVERT: E 57 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: E 95 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7348 (mtp-110) REVERT: E 314 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7986 (tt0) outliers start: 30 outliers final: 17 residues processed: 193 average time/residue: 1.4989 time to fit residues: 314.0245 Evaluate side-chains 196 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 34 optimal weight: 0.0030 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 92 ASN B 360 GLN D 246 GLN E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1833 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= 0.257 Angle : 0.611 7.440 20090 Z= 0.297 Chirality : 0.046 0.174 2230 Planarity : 0.004 0.031 2565 Dihedral : 9.447 128.849 2055 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.68 % Allowed : 9.29 % Favored : 89.03 % 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: 0.81 (0.20), residues: 1795 helix: 0.05 (0.18), residues: 790 sheet: -0.37 (0.27), residues: 320 loop : 2.07 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 340 HIS 0.006 0.001 HIS D 161 PHE 0.011 0.002 PHE D 262 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG E 62 *********************** 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 209 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.695 Fit side-chains REVERT: C 125 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: D 95 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7258 (mpp-170) REVERT: E 44 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7731 (mmm) REVERT: E 95 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7323 (mtp-110) REVERT: E 314 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7971 (tt0) outliers start: 26 outliers final: 14 residues processed: 197 average time/residue: 1.6120 time to fit residues: 343.9264 Evaluate side-chains 194 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 0.0040 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 92 ASN D 246 GLN E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14805 Z= 0.135 Angle : 0.540 6.806 20090 Z= 0.257 Chirality : 0.043 0.156 2230 Planarity : 0.003 0.033 2565 Dihedral : 8.790 121.074 2055 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.29 % Allowed : 9.94 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1795 helix: 0.17 (0.18), residues: 795 sheet: 0.00 (0.25), residues: 335 loop : 2.17 (0.27), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS D 161 PHE 0.008 0.001 PHE A 255 TYR 0.008 0.001 TYR C 143 ARG 0.003 0.000 ARG B 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 202 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 1.591 Fit side-chains REVERT: B 215 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8101 (mptm) REVERT: E 95 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7358 (mpp-170) REVERT: E 314 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7965 (tt0) outliers start: 20 outliers final: 7 residues processed: 194 average time/residue: 1.5306 time to fit residues: 321.9801 Evaluate side-chains 183 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.0000 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 85 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 92 ASN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14805 Z= 0.237 Angle : 0.594 7.377 20090 Z= 0.286 Chirality : 0.045 0.171 2230 Planarity : 0.004 0.031 2565 Dihedral : 9.145 123.545 2055 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.10 % Allowed : 10.26 % 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: 1.00 (0.20), residues: 1795 helix: 0.23 (0.18), residues: 790 sheet: -0.21 (0.27), residues: 315 loop : 2.07 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE D 262 TYR 0.010 0.001 TYR C 143 ARG 0.002 0.000 ARG B 95 *********************** 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 190 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.792 Fit side-chains REVERT: D 95 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7224 (mpp-170) REVERT: E 95 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7366 (mpp-170) REVERT: E 314 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7985 (tt0) outliers start: 17 outliers final: 11 residues processed: 184 average time/residue: 1.5188 time to fit residues: 303.2575 Evaluate side-chains 186 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 92 ASN B 360 GLN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14805 Z= 0.342 Angle : 0.651 7.887 20090 Z= 0.319 Chirality : 0.048 0.184 2230 Planarity : 0.004 0.038 2565 Dihedral : 9.545 129.407 2055 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.42 % Allowed : 9.94 % 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: 0.91 (0.20), residues: 1795 helix: 0.17 (0.18), residues: 790 sheet: -0.34 (0.27), residues: 320 loop : 2.06 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 340 HIS 0.004 0.001 HIS D 161 PHE 0.013 0.002 PHE B 262 TYR 0.011 0.001 TYR C 143 ARG 0.004 0.001 ARG E 210 *********************** 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 195 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.841 Fit side-chains REVERT: C 125 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: D 95 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7240 (mpp-170) REVERT: D 354 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7432 (pp30) REVERT: E 57 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: E 95 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7349 (mpp-170) REVERT: E 314 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7976 (tt0) outliers start: 22 outliers final: 12 residues processed: 188 average time/residue: 1.5725 time to fit residues: 320.7447 Evaluate side-chains 189 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 0.0010 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 92 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14805 Z= 0.154 Angle : 0.552 6.835 20090 Z= 0.263 Chirality : 0.044 0.165 2230 Planarity : 0.003 0.033 2565 Dihedral : 8.933 122.891 2055 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.71 % Allowed : 10.71 % Favored : 88.58 % 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: 1.07 (0.20), residues: 1795 helix: 0.25 (0.19), residues: 795 sheet: 0.01 (0.26), residues: 335 loop : 2.14 (0.27), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE A 255 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG B 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 189 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 1.720 Fit side-chains REVERT: B 215 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8138 (mptm) REVERT: E 95 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7363 (mpp-170) REVERT: E 314 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7964 (tt0) outliers start: 11 outliers final: 8 residues processed: 186 average time/residue: 1.5652 time to fit residues: 316.3479 Evaluate side-chains 181 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0170 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 0.0670 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS B 41 GLN B 92 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.100956 restraints weight = 14605.374| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.13 r_work: 0.3048 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14805 Z= 0.146 Angle : 0.543 6.826 20090 Z= 0.258 Chirality : 0.043 0.158 2230 Planarity : 0.003 0.033 2565 Dihedral : 8.608 119.344 2055 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.71 % Allowed : 10.84 % Favored : 88.45 % 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: 1.14 (0.20), residues: 1795 helix: 0.30 (0.19), residues: 795 sheet: 0.05 (0.26), residues: 335 loop : 2.18 (0.27), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.010 0.001 TYR C 143 ARG 0.003 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6109.09 seconds wall clock time: 108 minutes 29.53 seconds (6509.53 seconds total)