Starting phenix.real_space_refine on Tue Nov 19 00:30:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duu_47179/11_2024/9duu_47179_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duu_47179/11_2024/9duu_47179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duu_47179/11_2024/9duu_47179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duu_47179/11_2024/9duu_47179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duu_47179/11_2024/9duu_47179_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9duu_47179/11_2024/9duu_47179_neut.cif" } resolution = 3.4 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= 0.003 sd= 0.148 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 12 5.49 5 Mg 6 5.21 5 S 133 5.16 5 C 11327 2.51 5 N 3020 2.21 5 O 3455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17953 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" 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 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" 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 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" 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 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" 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 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" 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 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" 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 Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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} Chain: "F" 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} Time building chain proxies: 12.03, per 1000 atoms: 0.67 Number of scatterers: 17953 At special positions: 0 Unit cell: (79.328, 100.64, 224.96, 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 133 16.00 P 12 15.00 Mg 6 11.99 O 3455 8.00 N 3020 7.00 C 11327 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 - 3.00 Amino acid : True - 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 Links applied TRANS " TRP M 1 " - " ALA M 7 " " DTH M 4 " - " ALA M 3 " " TRP N 1 " - " ALA N 7 " " DTH N 4 " - " ALA N 3 " " TRP O 1 " - " ALA O 7 " " DTH O 4 " - " ALA O 3 " " TRP P 1 " - " ALA P 7 " " DTH P 4 " - " ALA P 3 " " TRP Q 1 " - " ALA Q 7 " " DTH Q 4 " - " ALA Q 3 " " TRP R 1 " - " ALA R 7 " " DTH R 4 " - " ALA R 3 " " TRP S 1 " - " ALA S 7 " " DTH S 4 " - " ALA S 3 " Time building additional restraints: 4.90 Conformation dependent library (CDL) restraints added in 2.3 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH M 4 " pdb=" CB DTH N 4 " pdb=" CB DTH O 4 " pdb=" CB DTH P 4 " pdb=" CB DTH Q 4 " pdb=" CB DTH R 4 " pdb=" CB DTH S 4 " Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 36 sheets defined 46.3% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.655A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.525A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.638A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.684A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.666A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.535A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.644A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.612A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.567A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.527A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.536A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.520A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.729A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.613A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 255' Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.318A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.765A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.142A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.546A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.683A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.655A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.298A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.896A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.867A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.529A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.528A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.799A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.693A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 232 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.536A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 288 through 295 removed outlier: 4.510A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.866A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.516A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.896A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 112 through 126 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 232 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 261 removed outlier: 3.583A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 258 through 261' Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.758A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.575A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 351 through 355 removed outlier: 3.700A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.323A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.126A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.300A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.744A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.423A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.020A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.133A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 5.973A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.113A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.531A pdb=" N HIS E 161 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 31 removed outlier: 4.233A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.800A pdb=" N THR F 160 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 5.860A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 821 hydrogen bonds defined for protein. 2154 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: 6.63 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2971 1.27 - 1.40: 4394 1.40 - 1.54: 10583 1.54 - 1.67: 167 1.67 - 1.81: 229 Bond restraints: 18344 Sorted by residual: bond pdb=" C LYS F 238 " pdb=" O LYS F 238 " ideal model delta sigma weight residual 1.234 1.135 0.099 1.25e-02 6.40e+03 6.23e+01 bond pdb=" C LYS B 238 " pdb=" O LYS B 238 " ideal model delta sigma weight residual 1.234 1.135 0.099 1.28e-02 6.10e+03 6.03e+01 bond pdb=" C LYS C 238 " pdb=" O LYS C 238 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.28e-02 6.10e+03 5.27e+01 bond pdb=" C LYS D 238 " pdb=" O LYS D 238 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.30e-02 5.92e+03 3.79e+01 bond pdb=" C LYS A 238 " pdb=" O LYS A 238 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.25e-02 6.40e+03 3.04e+01 ... (remaining 18339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 24210 2.12 - 4.23: 548 4.23 - 6.35: 107 6.35 - 8.46: 23 8.46 - 10.58: 17 Bond angle restraints: 24905 Sorted by residual: angle pdb=" N LYS D 238 " pdb=" CA LYS D 238 " pdb=" CB LYS D 238 " ideal model delta sigma weight residual 111.08 102.59 8.49 1.71e+00 3.42e-01 2.47e+01 angle pdb=" C HYP N 6 " pdb=" N ALA N 7 " pdb=" CA ALA N 7 " ideal model delta sigma weight residual 121.70 113.20 8.50 1.80e+00 3.09e-01 2.23e+01 angle pdb=" C HYP S 6 " pdb=" N ALA S 7 " pdb=" CA ALA S 7 " ideal model delta sigma weight residual 121.70 113.22 8.48 1.80e+00 3.09e-01 2.22e+01 angle pdb=" C HYP Q 6 " pdb=" N ALA Q 7 " pdb=" CA ALA Q 7 " ideal model delta sigma weight residual 121.70 113.26 8.44 1.80e+00 3.09e-01 2.20e+01 angle pdb=" C HYP M 6 " pdb=" N ALA M 7 " pdb=" CA ALA M 7 " ideal model delta sigma weight residual 121.70 113.30 8.40 1.80e+00 3.09e-01 2.18e+01 ... (remaining 24900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 9916 24.12 - 48.25: 1004 48.25 - 72.37: 117 72.37 - 96.49: 18 96.49 - 120.62: 5 Dihedral angle restraints: 11060 sinusoidal: 4495 harmonic: 6565 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.61 -120.62 1 2.00e+01 2.50e-03 3.62e+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 55.47 -115.47 1 2.00e+01 2.50e-03 3.43e+01 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 54.29 -114.29 1 2.00e+01 2.50e-03 3.39e+01 ... (remaining 11057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2198 0.048 - 0.096: 397 0.096 - 0.144: 169 0.144 - 0.192: 10 0.192 - 0.240: 2 Chirality restraints: 2776 Sorted by residual: chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA CYS S 5 " pdb=" N CYS S 5 " pdb=" C CYS S 5 " pdb=" CB CYS S 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA CYS R 5 " pdb=" N CYS R 5 " pdb=" C CYS R 5 " pdb=" CB CYS R 5 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 2773 not shown) Planarity restraints: 3170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 237 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU D 237 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU D 237 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS D 238 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 237 " 0.012 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C GLU C 237 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU C 237 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 238 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 237 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLU A 237 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU A 237 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 238 " 0.012 2.00e-02 2.50e+03 ... (remaining 3167 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 97 2.38 - 3.01: 9806 3.01 - 3.64: 26491 3.64 - 4.27: 40851 4.27 - 4.90: 71403 Nonbonded interactions: 148648 Sorted by model distance: nonbonded pdb=" CD1 TRP S 1 " pdb=" SG CYS S 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP N 1 " pdb=" SG CYS N 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP M 1 " pdb=" SG CYS M 5 " model vdw 1.753 3.620 nonbonded pdb=" CD1 TRP R 1 " pdb=" SG CYS R 5 " model vdw 1.753 3.620 nonbonded pdb=" CD1 TRP P 1 " pdb=" SG CYS P 5 " model vdw 1.753 3.620 ... (remaining 148643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 4.150 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: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.680 Find NCS groups from input model: 0.790 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.005 0.101 18344 Z= 0.340 Angle : 0.756 10.576 24905 Z= 0.382 Chirality : 0.045 0.240 2776 Planarity : 0.004 0.048 3156 Dihedral : 17.764 120.617 6818 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.37 % Favored : 95.36 % Rotamer: Outliers : 0.85 % Allowed : 29.70 % Favored : 69.45 % Cbeta Deviations : 0.14 % 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: 0.69 (0.19), residues: 2196 helix: 1.20 (0.18), residues: 930 sheet: 0.10 (0.34), residues: 282 loop : -0.04 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 1 HIS 0.001 0.000 HIS A 161 PHE 0.007 0.001 PHE B 200 TYR 0.009 0.001 TYR E 279 ARG 0.002 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 215 average time/residue: 0.2599 time to fit residues: 90.5324 Evaluate side-chains 210 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain M residue 5 CYS Chi-restraints excluded: chain N residue 5 CYS Chi-restraints excluded: chain O residue 5 CYS Chi-restraints excluded: chain P residue 5 CYS Chi-restraints excluded: chain Q residue 5 CYS Chi-restraints excluded: chain R residue 5 CYS Chi-restraints excluded: chain S residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 174 optimal weight: 0.0270 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 129 optimal weight: 0.4980 chunk 201 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 12 ASN D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18344 Z= 0.199 Angle : 0.584 6.450 24905 Z= 0.276 Chirality : 0.045 0.175 2776 Planarity : 0.004 0.032 3156 Dihedral : 9.299 118.865 2636 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 3.12 % Allowed : 26.37 % Favored : 70.51 % 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: 0.76 (0.19), residues: 2196 helix: 1.13 (0.18), residues: 948 sheet: 0.14 (0.29), residues: 354 loop : 0.15 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 1 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE D 255 TYR 0.008 0.001 TYR A 198 ARG 0.002 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.6522 (t80) REVERT: B 99 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: C 72 GLU cc_start: 0.8036 (pm20) cc_final: 0.7572 (pt0) REVERT: E 364 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7439 (mt-10) outliers start: 59 outliers final: 24 residues processed: 242 average time/residue: 0.2591 time to fit residues: 101.8426 Evaluate side-chains 218 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 179 optimal weight: 0.0980 chunk 200 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18344 Z= 0.284 Angle : 0.606 6.794 24905 Z= 0.287 Chirality : 0.047 0.241 2776 Planarity : 0.004 0.033 3156 Dihedral : 8.590 116.154 2621 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.01 % Favored : 94.72 % Rotamer: Outliers : 3.54 % Allowed : 25.21 % Favored : 71.25 % 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 (0.19), residues: 2196 helix: 1.02 (0.18), residues: 948 sheet: -0.10 (0.29), residues: 354 loop : 0.10 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 340 HIS 0.005 0.001 HIS A 161 PHE 0.007 0.001 PHE C 255 TYR 0.009 0.001 TYR A 198 ARG 0.003 0.000 ARG F 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 197 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 124 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7061 (t80) REVERT: B 99 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: C 72 GLU cc_start: 0.8261 (pm20) cc_final: 0.8047 (pt0) REVERT: C 82 MET cc_start: 0.8726 (mmm) cc_final: 0.8511 (tpt) REVERT: C 283 MET cc_start: 0.7645 (ttm) cc_final: 0.7354 (mmt) REVERT: C 305 MET cc_start: 0.9123 (mmm) cc_final: 0.8820 (mmm) REVERT: E 115 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8305 (t0) REVERT: E 178 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8272 (tp) outliers start: 67 outliers final: 36 residues processed: 246 average time/residue: 0.2706 time to fit residues: 108.4671 Evaluate side-chains 230 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18344 Z= 0.224 Angle : 0.576 6.484 24905 Z= 0.270 Chirality : 0.046 0.235 2776 Planarity : 0.003 0.032 3156 Dihedral : 8.481 116.797 2621 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.10 % Favored : 94.63 % Rotamer: Outliers : 3.75 % Allowed : 25.11 % Favored : 71.14 % 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: 0.68 (0.19), residues: 2196 helix: 1.14 (0.18), residues: 942 sheet: -0.17 (0.28), residues: 366 loop : 0.16 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.010 0.001 TYR D 279 ARG 0.005 0.000 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 124 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.6905 (t80) REVERT: B 99 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: C 82 MET cc_start: 0.8799 (mmm) cc_final: 0.8585 (tpt) REVERT: D 132 MET cc_start: 0.8953 (tmm) cc_final: 0.8578 (ttp) REVERT: D 283 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6596 (ttm) REVERT: E 178 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (tp) REVERT: E 346 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8338 (tp) REVERT: F 123 MET cc_start: 0.8023 (tpp) cc_final: 0.7770 (mtp) outliers start: 71 outliers final: 45 residues processed: 254 average time/residue: 0.2624 time to fit residues: 107.8464 Evaluate side-chains 238 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 192 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18344 Z= 0.179 Angle : 0.554 6.413 24905 Z= 0.258 Chirality : 0.045 0.233 2776 Planarity : 0.003 0.031 3156 Dihedral : 8.308 116.079 2621 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.51 % Favored : 95.22 % Rotamer: Outliers : 3.75 % Allowed : 25.37 % Favored : 70.88 % 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: 0.76 (0.19), residues: 2196 helix: 1.24 (0.18), residues: 942 sheet: -0.25 (0.27), residues: 378 loop : 0.22 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE E 255 TYR 0.005 0.001 TYR D 279 ARG 0.003 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 124 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.6816 (t80) REVERT: B 99 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: D 132 MET cc_start: 0.9022 (tmm) cc_final: 0.8624 (ttp) REVERT: E 115 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8279 (t0) REVERT: E 178 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8152 (tp) REVERT: E 346 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8315 (tp) outliers start: 71 outliers final: 45 residues processed: 254 average time/residue: 0.2523 time to fit residues: 105.2532 Evaluate side-chains 245 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.2980 chunk 193 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18344 Z= 0.264 Angle : 0.586 6.802 24905 Z= 0.274 Chirality : 0.047 0.242 2776 Planarity : 0.004 0.033 3156 Dihedral : 8.298 114.245 2621 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.28 % Favored : 94.44 % Rotamer: Outliers : 4.02 % Allowed : 24.68 % Favored : 71.30 % 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: 0.62 (0.19), residues: 2196 helix: 1.13 (0.18), residues: 942 sheet: -0.41 (0.26), residues: 378 loop : 0.19 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.009 0.001 TYR A 133 ARG 0.004 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 196 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8230 (mp) REVERT: A 124 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 334 GLU cc_start: 0.7666 (pm20) cc_final: 0.7407 (pm20) REVERT: B 99 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: E 115 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8357 (t0) REVERT: E 178 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8194 (tp) outliers start: 76 outliers final: 55 residues processed: 255 average time/residue: 0.2541 time to fit residues: 106.3993 Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 180 optimal weight: 0.0010 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18344 Z= 0.251 Angle : 0.584 6.607 24905 Z= 0.273 Chirality : 0.047 0.244 2776 Planarity : 0.004 0.035 3156 Dihedral : 8.306 115.239 2621 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 3.91 % Allowed : 24.42 % Favored : 71.67 % 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: 0.58 (0.19), residues: 2196 helix: 1.13 (0.18), residues: 942 sheet: -0.52 (0.26), residues: 378 loop : 0.18 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.004 0.001 HIS A 161 PHE 0.008 0.001 PHE A 255 TYR 0.007 0.001 TYR A 133 ARG 0.002 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 191 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 124 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7661 (t80) REVERT: B 99 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: D 132 MET cc_start: 0.8949 (tmm) cc_final: 0.8485 (ttp) REVERT: D 283 MET cc_start: 0.7756 (ttm) cc_final: 0.7278 (mtp) REVERT: E 95 ARG cc_start: 0.8583 (ttm110) cc_final: 0.8236 (ttm110) REVERT: E 115 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8371 (t0) REVERT: E 178 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8182 (tp) REVERT: E 346 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8278 (tp) outliers start: 74 outliers final: 54 residues processed: 250 average time/residue: 0.2521 time to fit residues: 103.8454 Evaluate side-chains 246 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18344 Z= 0.244 Angle : 0.582 6.616 24905 Z= 0.272 Chirality : 0.047 0.245 2776 Planarity : 0.004 0.036 3156 Dihedral : 8.304 115.401 2621 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.15 % Favored : 94.58 % Rotamer: Outliers : 4.02 % Allowed : 24.21 % Favored : 71.78 % 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: 0.58 (0.19), residues: 2196 helix: 1.13 (0.18), residues: 942 sheet: -0.55 (0.26), residues: 378 loop : 0.18 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.007 0.001 TYR A 133 ARG 0.002 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 195 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 124 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7022 (t80) REVERT: B 99 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: D 132 MET cc_start: 0.9004 (tmm) cc_final: 0.8528 (ttp) REVERT: E 115 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8381 (t0) REVERT: E 178 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8172 (tp) REVERT: E 346 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8279 (tp) outliers start: 76 outliers final: 57 residues processed: 252 average time/residue: 0.2540 time to fit residues: 106.6313 Evaluate side-chains 254 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18344 Z= 0.311 Angle : 0.612 7.123 24905 Z= 0.288 Chirality : 0.048 0.249 2776 Planarity : 0.004 0.035 3156 Dihedral : 8.349 114.343 2621 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.15 % Favored : 94.58 % Rotamer: Outliers : 3.86 % Allowed : 24.37 % Favored : 71.78 % 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: 2196 helix: 1.03 (0.18), residues: 942 sheet: -0.62 (0.25), residues: 378 loop : 0.09 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.009 0.001 TYR E 279 ARG 0.004 0.000 ARG F 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 196 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 124 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.6886 (t80) REVERT: A 334 GLU cc_start: 0.7589 (pm20) cc_final: 0.7363 (pm20) REVERT: B 99 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: D 132 MET cc_start: 0.9044 (tmm) cc_final: 0.8585 (ttp) REVERT: E 95 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8309 (ttm110) REVERT: E 115 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8386 (t0) REVERT: E 178 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8224 (tp) outliers start: 73 outliers final: 62 residues processed: 253 average time/residue: 0.2500 time to fit residues: 104.1870 Evaluate side-chains 259 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 221 optimal weight: 0.3980 chunk 203 optimal weight: 0.0980 chunk 176 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18344 Z= 0.194 Angle : 0.570 6.489 24905 Z= 0.266 Chirality : 0.046 0.244 2776 Planarity : 0.003 0.035 3156 Dihedral : 8.259 114.822 2621 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.96 % Favored : 94.76 % Rotamer: Outliers : 3.65 % Allowed : 24.58 % Favored : 71.78 % 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 (0.19), residues: 2196 helix: 1.17 (0.18), residues: 942 sheet: -0.56 (0.26), residues: 378 loop : 0.17 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE A 255 TYR 0.007 0.001 TYR E 279 ARG 0.003 0.000 ARG F 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 197 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8229 (mp) REVERT: A 124 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.6863 (t80) REVERT: B 99 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8211 (pm20) REVERT: D 132 MET cc_start: 0.9018 (tmm) cc_final: 0.8525 (ttp) REVERT: D 283 MET cc_start: 0.7735 (ttm) cc_final: 0.7441 (mmt) REVERT: E 115 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8391 (t0) REVERT: E 178 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8134 (tp) outliers start: 69 outliers final: 56 residues processed: 250 average time/residue: 0.2564 time to fit residues: 105.4162 Evaluate side-chains 256 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 12 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.095232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.084394 restraints weight = 22438.073| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 1.21 r_work: 0.2670 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18344 Z= 0.300 Angle : 0.610 6.829 24905 Z= 0.287 Chirality : 0.048 0.248 2776 Planarity : 0.004 0.036 3156 Dihedral : 8.316 113.387 2621 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.33 % Favored : 94.40 % Rotamer: Outliers : 3.59 % Allowed : 24.79 % Favored : 71.62 % 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: 0.43 (0.19), residues: 2196 helix: 1.04 (0.18), residues: 942 sheet: -0.67 (0.25), residues: 378 loop : 0.08 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE E 255 TYR 0.009 0.001 TYR E 279 ARG 0.004 0.000 ARG F 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3497.37 seconds wall clock time: 65 minutes 16.05 seconds (3916.05 seconds total)