Starting phenix.real_space_refine on Fri Feb 16 09:04:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8v_24321/02_2024/7r8v_24321_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8v_24321/02_2024/7r8v_24321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8v_24321/02_2024/7r8v_24321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8v_24321/02_2024/7r8v_24321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8v_24321/02_2024/7r8v_24321_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8v_24321/02_2024/7r8v_24321_updated.pdb" } resolution = 2.82 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= 0.003 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 110 5.16 5 C 9360 2.51 5 N 2510 2.21 5 O 2850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 72": "OE1" <-> "OE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14845 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 Conformer: "B" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 bond proxies already assigned to first conformer: 2921 Chain: "A" Number of atoms: 2941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 Conformer: "B" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 bond proxies already assigned to first conformer: 2921 Chain: "C" Number of atoms: 2941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 Conformer: "B" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 bond proxies already assigned to first conformer: 2921 Chain: "D" Number of atoms: 2941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 Conformer: "B" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 bond proxies already assigned to first conformer: 2921 Chain: "E" Number of atoms: 2941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 Conformer: "B" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 bond proxies already assigned to first conformer: 2921 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: "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: "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: "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} Residues with excluded nonbonded symmetry interactions: 30 residue: pdb=" N AVAL B 45 " occ=0.80 ... (12 atoms not shown) pdb=" CG2BVAL B 45 " occ=0.20 residue: pdb=" N AGLY B 46 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 46 " occ=0.50 residue: pdb=" N AMET B 47 " occ=0.80 ... (14 atoms not shown) pdb=" CE BMET B 47 " occ=0.20 residue: pdb=" N AGLY B 48 " occ=0.80 ... (6 atoms not shown) pdb=" O BGLY B 48 " occ=0.20 residue: pdb=" N AGLN B 49 " occ=0.80 ... (16 atoms not shown) pdb=" NE2BGLN B 49 " occ=0.20 residue: pdb=" N ALYS B 50 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 50 " occ=0.50 residue: pdb=" N AVAL A 45 " occ=0.80 ... (12 atoms not shown) pdb=" CG2BVAL A 45 " occ=0.20 residue: pdb=" N AGLY A 46 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 46 " occ=0.50 residue: pdb=" N AMET A 47 " occ=0.80 ... (14 atoms not shown) pdb=" CE BMET A 47 " occ=0.20 residue: pdb=" N AGLY A 48 " occ=0.80 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.20 residue: pdb=" N AGLN A 49 " occ=0.80 ... (16 atoms not shown) pdb=" NE2BGLN A 49 " occ=0.20 residue: pdb=" N ALYS A 50 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 50 " occ=0.50 ... (remaining 18 not shown) Time building chain proxies: 14.58, per 1000 atoms: 0.98 Number of scatterers: 14845 At special positions: 0 Unit cell: (89.61, 93.73, 196.73, 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 110 16.00 P 10 15.00 Mg 5 11.99 O 2850 8.00 N 2510 7.00 C 9360 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: 5.52 Conformation dependent library (CDL) restraints added in 5.1 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 20 sheets defined 42.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 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: 3.925A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.821A 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: 3.730A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.444A 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: 3.675A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 292 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.509A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 Proline residue: B 367 - end of helix removed outlier: 5.555A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 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: 3.926A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.820A 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: 3.730A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.443A 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: 3.674A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 292 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.509A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 Proline residue: A 367 - end of helix removed outlier: 5.555A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 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: 3.925A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.820A 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: 3.730A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.443A 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: 3.675A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 347 removed outlier: 3.510A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.555A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 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: 3.925A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.820A 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: 3.731A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.444A 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: 3.676A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 292 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 347 removed outlier: 3.510A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 373 Proline residue: D 367 - end of helix removed outlier: 5.556A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 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: 3.925A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.820A 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: 3.730A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.444A 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: 3.675A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP E 292 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 347 removed outlier: 3.510A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 373 Proline residue: E 367 - end of helix removed outlier: 5.554A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.901A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'B' and resid 298 through 300 Processing sheet with id= D, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.902A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'A' and resid 298 through 300 Processing sheet with id= H, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.901A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 298 through 300 Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.901A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 298 through 300 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: 6.901A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 298 through 300 Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 555 hydrogen bonds defined for protein. 1365 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: 4.61 Time building geometry restraints manager: 6.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4833 1.34 - 1.46: 3130 1.46 - 1.58: 6997 1.58 - 1.69: 15 1.69 - 1.81: 195 Bond restraints: 15170 Sorted by residual: bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.14e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.89e+00 ... (remaining 15165 not shown) Histogram of bond angle deviations from ideal: 98.86 - 106.33: 559 106.33 - 113.80: 8453 113.80 - 121.26: 7682 121.26 - 128.73: 3796 128.73 - 136.19: 95 Bond angle restraints: 20585 Sorted by residual: angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 114.64 -4.14 1.70e+00 3.46e-01 5.94e+00 angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 114.62 -4.12 1.70e+00 3.46e-01 5.88e+00 angle pdb=" N HIC E 73 " pdb=" CA HIC E 73 " pdb=" CB HIC E 73 " ideal model delta sigma weight residual 110.50 114.60 -4.10 1.70e+00 3.46e-01 5.82e+00 angle pdb=" N HIC A 73 " pdb=" CA HIC A 73 " pdb=" CB HIC A 73 " ideal model delta sigma weight residual 110.50 114.60 -4.10 1.70e+00 3.46e-01 5.80e+00 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 114.59 -4.09 1.70e+00 3.46e-01 5.80e+00 ... (remaining 20580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.98: 8873 29.98 - 59.95: 222 59.95 - 89.93: 15 89.93 - 119.90: 5 119.90 - 149.88: 10 Dihedral angle restraints: 9125 sinusoidal: 3690 harmonic: 5435 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.13 149.88 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.13 149.87 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 150.14 149.86 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1278 0.028 - 0.056: 607 0.056 - 0.085: 201 0.085 - 0.113: 152 0.113 - 0.141: 42 Chirality restraints: 2280 Sorted by residual: chirality pdb=" CA ILE B 165 " pdb=" N ILE B 165 " pdb=" C ILE B 165 " pdb=" CB ILE B 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE C 165 " pdb=" N ILE C 165 " pdb=" C ILE C 165 " pdb=" CB ILE C 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE E 165 " pdb=" N ILE E 165 " pdb=" C ILE E 165 " pdb=" CB ILE E 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 2277 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 366 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO E 367 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO E 367 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 367 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 366 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 367 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO B 367 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.018 5.00e-02 4.00e+02 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 126 2.60 - 3.18: 12044 3.18 - 3.75: 22966 3.75 - 4.33: 33872 4.33 - 4.90: 56291 Nonbonded interactions: 125299 Sorted by model distance: nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.028 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.029 2.170 nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.029 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.029 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.029 2.170 ... (remaining 125294 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' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'B' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'C' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'D' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'E' and (resid 5 through 44 or resid 51 through 375 or resid 401 through \ 402)) } 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=0.20 max=1.00 mean=0.99 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: 9.330 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: 31.690 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 51.300 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.003 0.057 15170 Z= 0.201 Angle : 0.544 5.598 20585 Z= 0.268 Chirality : 0.044 0.141 2280 Planarity : 0.004 0.032 2635 Dihedral : 14.128 149.878 5655 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1870 helix: 0.58 (0.19), residues: 795 sheet: 0.69 (0.29), residues: 325 loop : 0.76 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 79 HIS 0.002 0.001 HIS C 161 PHE 0.006 0.001 PHE C 255 TYR 0.008 0.001 TYR A 143 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.833 Fit side-chains REVERT: A 299 MET cc_start: 0.8577 (mtm) cc_final: 0.8345 (mtm) REVERT: C 123 MET cc_start: 0.9069 (mmt) cc_final: 0.8412 (mmt) REVERT: C 283 MET cc_start: 0.8924 (mmm) cc_final: 0.8703 (mmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 1.8003 time to fit residues: 357.8906 Evaluate side-chains 125 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 246 GLN E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15170 Z= 0.257 Angle : 0.571 6.322 20585 Z= 0.280 Chirality : 0.046 0.150 2280 Planarity : 0.005 0.044 2635 Dihedral : 11.173 148.785 2120 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.14 % Allowed : 5.24 % Favored : 93.63 % 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: 0.71 (0.20), residues: 1870 helix: 0.38 (0.19), residues: 795 sheet: 0.77 (0.28), residues: 335 loop : 0.70 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.009 0.001 PHE B 375 TYR 0.011 0.001 TYR D 69 ARG 0.010 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.705 Fit side-chains REVERT: A 44 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7879 (mpt) REVERT: A 107 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: A 299 MET cc_start: 0.8561 (mtm) cc_final: 0.8305 (mtm) REVERT: A 328 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8243 (mtmt) REVERT: C 123 MET cc_start: 0.9093 (mmt) cc_final: 0.8380 (mmt) outliers start: 18 outliers final: 6 residues processed: 144 average time/residue: 1.7168 time to fit residues: 266.4946 Evaluate side-chains 132 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 168 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15170 Z= 0.227 Angle : 0.553 6.385 20585 Z= 0.268 Chirality : 0.045 0.152 2280 Planarity : 0.004 0.043 2635 Dihedral : 10.973 158.551 2120 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.95 % Allowed : 6.12 % Favored : 92.93 % 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: 0.65 (0.19), residues: 1870 helix: 0.26 (0.19), residues: 795 sheet: 0.94 (0.28), residues: 330 loop : 0.65 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.008 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.725 Fit side-chains REVERT: A 44 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7972 (mpt) REVERT: A 95 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7500 (mtp180) REVERT: A 107 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8405 (tt0) REVERT: A 299 MET cc_start: 0.8546 (mtm) cc_final: 0.8278 (mtm) REVERT: C 123 MET cc_start: 0.9066 (mmt) cc_final: 0.8297 (mmt) REVERT: C 313 MET cc_start: 0.8989 (mmm) cc_final: 0.8708 (mmm) REVERT: D 176 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8031 (mtm) outliers start: 15 outliers final: 4 residues processed: 138 average time/residue: 1.8690 time to fit residues: 276.7249 Evaluate side-chains 131 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15170 Z= 0.272 Angle : 0.572 6.570 20585 Z= 0.278 Chirality : 0.046 0.155 2280 Planarity : 0.004 0.043 2635 Dihedral : 10.984 164.258 2120 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.95 % Allowed : 6.81 % Favored : 92.24 % 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: 0.56 (0.19), residues: 1870 helix: 0.14 (0.19), residues: 795 sheet: 0.96 (0.28), residues: 330 loop : 0.62 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 340 HIS 0.006 0.001 HIS D 161 PHE 0.009 0.001 PHE D 31 TYR 0.010 0.001 TYR D 69 ARG 0.010 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.562 Fit side-chains REVERT: A 44 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7904 (mpt) REVERT: A 95 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7485 (mtp180) REVERT: A 107 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: C 123 MET cc_start: 0.9057 (mmt) cc_final: 0.8222 (mmt) outliers start: 15 outliers final: 9 residues processed: 134 average time/residue: 1.7062 time to fit residues: 246.3017 Evaluate side-chains 135 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 372 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN E 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15170 Z= 0.342 Angle : 0.600 6.898 20585 Z= 0.293 Chirality : 0.048 0.159 2280 Planarity : 0.005 0.042 2635 Dihedral : 11.080 171.607 2120 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.01 % Allowed : 7.32 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 1870 helix: 0.07 (0.19), residues: 790 sheet: 0.95 (0.28), residues: 330 loop : 0.49 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 340 HIS 0.006 0.001 HIS D 161 PHE 0.010 0.001 PHE C 31 TYR 0.012 0.001 TYR D 69 ARG 0.009 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.707 Fit side-chains REVERT: A 44 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8002 (mpt) REVERT: A 95 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7474 (mtp180) REVERT: A 107 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: C 123 MET cc_start: 0.9019 (mmt) cc_final: 0.8183 (mmt) REVERT: C 313 MET cc_start: 0.8981 (mmm) cc_final: 0.8724 (mmm) outliers start: 16 outliers final: 8 residues processed: 130 average time/residue: 1.8122 time to fit residues: 253.5037 Evaluate side-chains 133 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 372 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN D 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15170 Z= 0.287 Angle : 0.575 6.800 20585 Z= 0.279 Chirality : 0.047 0.154 2280 Planarity : 0.004 0.042 2635 Dihedral : 11.026 175.545 2120 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.14 % Allowed : 7.38 % Favored : 91.48 % 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: 0.49 (0.19), residues: 1870 helix: 0.08 (0.19), residues: 790 sheet: 0.99 (0.28), residues: 340 loop : 0.54 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 340 HIS 0.006 0.001 HIS D 161 PHE 0.010 0.001 PHE D 31 TYR 0.010 0.001 TYR D 69 ARG 0.009 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.548 Fit side-chains REVERT: A 44 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7987 (mpt) REVERT: A 95 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7478 (mtp180) REVERT: A 107 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: C 123 MET cc_start: 0.8997 (mmt) cc_final: 0.8130 (mmt) REVERT: C 372 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7869 (ptp90) REVERT: D 328 LYS cc_start: 0.8436 (mptt) cc_final: 0.8223 (mmtm) REVERT: D 369 ILE cc_start: 0.9362 (tp) cc_final: 0.9053 (tp) outliers start: 18 outliers final: 10 residues processed: 130 average time/residue: 1.7573 time to fit residues: 245.7646 Evaluate side-chains 136 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 372 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15170 Z= 0.268 Angle : 0.570 6.718 20585 Z= 0.277 Chirality : 0.046 0.155 2280 Planarity : 0.004 0.042 2635 Dihedral : 10.967 177.531 2120 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.14 % Allowed : 7.57 % Favored : 91.29 % 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: 0.56 (0.20), residues: 1870 helix: 0.13 (0.19), residues: 785 sheet: 1.00 (0.28), residues: 340 loop : 0.61 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 340 HIS 0.006 0.001 HIS D 161 PHE 0.010 0.001 PHE D 31 TYR 0.009 0.001 TYR D 69 ARG 0.009 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.732 Fit side-chains REVERT: A 44 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7948 (mpt) REVERT: A 95 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7482 (mtp180) REVERT: A 107 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: C 123 MET cc_start: 0.8986 (mmt) cc_final: 0.8133 (mmt) REVERT: C 292 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: C 372 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7870 (ptp90) REVERT: D 328 LYS cc_start: 0.8452 (mptt) cc_final: 0.8234 (mmtm) REVERT: D 369 ILE cc_start: 0.9356 (tp) cc_final: 0.9051 (tp) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 1.7844 time to fit residues: 249.8130 Evaluate side-chains 140 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 372 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.0030 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN D 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15170 Z= 0.217 Angle : 0.549 6.566 20585 Z= 0.264 Chirality : 0.045 0.152 2280 Planarity : 0.004 0.042 2635 Dihedral : 10.841 178.427 2120 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.20 % Allowed : 7.57 % Favored : 91.23 % 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: 0.63 (0.20), residues: 1870 helix: 0.19 (0.19), residues: 785 sheet: 1.01 (0.28), residues: 340 loop : 0.66 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS D 161 PHE 0.009 0.001 PHE D 31 TYR 0.008 0.001 TYR D 69 ARG 0.010 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.845 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7930 (mpt) REVERT: A 95 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7465 (mtp180) REVERT: A 107 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: C 123 MET cc_start: 0.8975 (mmt) cc_final: 0.8138 (mmt) REVERT: C 292 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: C 372 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7786 (ptp90) REVERT: D 176 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8053 (mtm) REVERT: D 369 ILE cc_start: 0.9341 (tp) cc_final: 0.9036 (tp) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 1.8282 time to fit residues: 254.1178 Evaluate side-chains 138 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 372 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 157 optimal weight: 0.0670 chunk 165 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15170 Z= 0.243 Angle : 0.562 6.706 20585 Z= 0.271 Chirality : 0.045 0.154 2280 Planarity : 0.004 0.042 2635 Dihedral : 10.797 179.089 2120 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.20 % Allowed : 7.70 % Favored : 91.10 % 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: 0.61 (0.20), residues: 1870 helix: 0.18 (0.19), residues: 785 sheet: 0.99 (0.28), residues: 340 loop : 0.65 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.009 0.001 PHE C 31 TYR 0.009 0.001 TYR D 69 ARG 0.009 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.723 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7934 (mpt) REVERT: A 95 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7473 (mtp180) REVERT: A 107 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: C 123 MET cc_start: 0.8972 (mmt) cc_final: 0.8131 (mmt) REVERT: C 292 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: C 372 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7790 (ptp90) REVERT: D 176 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8106 (mtm) REVERT: D 369 ILE cc_start: 0.9341 (tp) cc_final: 0.9039 (tp) outliers start: 19 outliers final: 12 residues processed: 129 average time/residue: 1.7896 time to fit residues: 248.5761 Evaluate side-chains 142 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 372 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 184 optimal weight: 0.3980 chunk 169 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15170 Z= 0.260 Angle : 0.567 6.825 20585 Z= 0.274 Chirality : 0.046 0.155 2280 Planarity : 0.004 0.042 2635 Dihedral : 10.770 179.726 2120 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.14 % Allowed : 7.76 % Favored : 91.10 % 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: 0.60 (0.20), residues: 1870 helix: 0.16 (0.19), residues: 785 sheet: 0.98 (0.28), residues: 340 loop : 0.64 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.006 0.001 HIS D 161 PHE 0.010 0.001 PHE C 31 TYR 0.010 0.001 TYR D 69 ARG 0.010 0.000 ARG E 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.790 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7942 (mpt) REVERT: A 95 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7470 (mtp180) REVERT: A 107 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: C 123 MET cc_start: 0.8976 (mmt) cc_final: 0.8221 (mmt) REVERT: C 292 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: C 372 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7810 (ptp90) REVERT: D 369 ILE cc_start: 0.9343 (tp) cc_final: 0.9039 (tp) outliers start: 18 outliers final: 13 residues processed: 129 average time/residue: 1.7798 time to fit residues: 247.1879 Evaluate side-chains 139 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 372 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 0.0570 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.088826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.068810 restraints weight = 59714.066| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.99 r_work: 0.2543 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15170 Z= 0.215 Angle : 0.552 6.576 20585 Z= 0.265 Chirality : 0.045 0.152 2280 Planarity : 0.004 0.042 2635 Dihedral : 10.669 179.937 2120 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.14 % Allowed : 7.76 % Favored : 91.10 % 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: 0.65 (0.20), residues: 1870 helix: 0.17 (0.19), residues: 790 sheet: 0.99 (0.28), residues: 340 loop : 0.72 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS D 161 PHE 0.009 0.001 PHE D 31 TYR 0.008 0.001 TYR D 69 ARG 0.010 0.000 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5299.88 seconds wall clock time: 96 minutes 5.23 seconds (5765.23 seconds total)