Starting phenix.real_space_refine on Sat Mar 16 15:15:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t20_10364/03_2024/6t20_10364_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t20_10364/03_2024/6t20_10364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t20_10364/03_2024/6t20_10364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t20_10364/03_2024/6t20_10364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t20_10364/03_2024/6t20_10364_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t20_10364/03_2024/6t20_10364_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9410 2.51 5 N 2510 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 196": "NH1" <-> "NH2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14915 Number of models: 1 Model: "" Number of chains: 15 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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 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} Time building chain proxies: 8.54, per 1000 atoms: 0.57 Number of scatterers: 14915 At special positions: 0 Unit cell: (98.56, 92.96, 192.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 10 15.00 Mg 5 11.99 O 2870 8.00 N 2510 7.00 C 9410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.91 Conformation dependent library (CDL) restraints added in 2.9 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH F 4 " pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3490 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 25 sheets defined 43.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.557A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.812A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 5.098A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.497A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.436A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.558A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.812A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 5.097A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 295 removed outlier: 4.496A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.436A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.558A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.811A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 5.097A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.496A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.435A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.558A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.811A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 5.096A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 295 removed outlier: 4.497A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.436A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.557A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 removed outlier: 3.811A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 5.097A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 295 removed outlier: 4.496A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.435A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.195A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 11 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.194A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= L, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.195A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= P, first strand: chain 'D' and resid 8 through 11 Processing sheet with id= Q, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= R, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= S, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.194A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'E' and resid 8 through 11 Processing sheet with id= V, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= X, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.195A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 238 through 241 585 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3455 1.32 - 1.44: 3694 1.44 - 1.56: 7901 1.56 - 1.68: 5 1.68 - 1.80: 190 Bond restraints: 15245 Sorted by residual: bond pdb=" CA EEP F 2 " pdb=" C EEP F 2 " ideal model delta sigma weight residual 1.572 1.453 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" CA EEP G 2 " pdb=" C EEP G 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 15240 not shown) Histogram of bond angle deviations from ideal: 94.53 - 102.71: 115 102.71 - 110.88: 5952 110.88 - 119.06: 6750 119.06 - 127.24: 7714 127.24 - 135.42: 174 Bond angle restraints: 20705 Sorted by residual: angle pdb=" C HIS E 101 " pdb=" N PRO E 102 " pdb=" CA PRO E 102 " ideal model delta sigma weight residual 119.78 129.31 -9.53 1.03e+00 9.43e-01 8.56e+01 angle pdb=" C HIS A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 119.78 129.31 -9.53 1.03e+00 9.43e-01 8.56e+01 angle pdb=" C HIS C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta sigma weight residual 119.78 129.29 -9.51 1.03e+00 9.43e-01 8.52e+01 angle pdb=" C HIS B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta sigma weight residual 119.78 129.27 -9.49 1.03e+00 9.43e-01 8.50e+01 angle pdb=" C HIS D 101 " pdb=" N PRO D 102 " pdb=" CA PRO D 102 " ideal model delta sigma weight residual 119.78 129.27 -9.49 1.03e+00 9.43e-01 8.49e+01 ... (remaining 20700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 8965 27.06 - 54.12: 135 54.12 - 81.19: 50 81.19 - 108.25: 0 108.25 - 135.31: 10 Dihedral angle restraints: 9160 sinusoidal: 3710 harmonic: 5450 Sorted by residual: dihedral pdb=" CA HYP H 6 " pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta harmonic sigma weight residual 180.00 147.87 32.13 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA HYP G 6 " pdb=" C HYP G 6 " pdb=" N ALA G 7 " pdb=" CA ALA G 7 " ideal model delta harmonic sigma weight residual 180.00 147.90 32.10 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA HYP J 6 " pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta harmonic sigma weight residual 180.00 147.91 32.09 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 9157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 788 0.049 - 0.097: 849 0.097 - 0.146: 450 0.146 - 0.194: 168 0.194 - 0.243: 50 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA ASN B 296 " pdb=" N ASN B 296 " pdb=" C ASN B 296 " pdb=" CB ASN B 296 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASN D 296 " pdb=" N ASN D 296 " pdb=" C ASN D 296 " pdb=" CB ASN D 296 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ASN E 296 " pdb=" N ASN E 296 " pdb=" C ASN E 296 " pdb=" CB ASN E 296 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2302 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 306 " -0.089 2.00e-02 2.50e+03 5.24e-02 5.50e+01 pdb=" CG TYR A 306 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 306 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 306 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR A 306 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 306 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 306 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 306 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.089 2.00e-02 2.50e+03 5.24e-02 5.48e+01 pdb=" CG TYR C 306 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 306 " 0.089 2.00e-02 2.50e+03 5.23e-02 5.48e+01 pdb=" CG TYR D 306 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 306 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR D 306 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR D 306 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR D 306 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR D 306 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR D 306 " 0.090 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 20 2.03 - 2.75: 2912 2.75 - 3.47: 21780 3.47 - 4.18: 37858 4.18 - 4.90: 63645 Nonbonded interactions: 126215 Sorted by model distance: nonbonded pdb=" N TRP F 1 " pdb=" C ALA F 7 " model vdw 1.317 3.350 nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.318 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.318 3.350 nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.318 3.350 nonbonded pdb=" N TRP G 1 " pdb=" C ALA G 7 " model vdw 1.318 3.350 ... (remaining 126210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 4.200 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 42.620 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.019 0.119 15245 Z= 1.225 Angle : 1.686 12.055 20705 Z= 1.116 Chirality : 0.089 0.243 2305 Planarity : 0.006 0.052 2630 Dihedral : 12.279 135.311 5670 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 1830 helix: -0.92 (0.15), residues: 750 sheet: -0.26 (0.29), residues: 290 loop : -0.50 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.006 TRP A 340 HIS 0.007 0.003 HIS A 88 PHE 0.013 0.004 PHE E 31 TYR 0.090 0.009 TYR A 306 ARG 0.005 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 580 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.7544 (p0) cc_final: 0.7267 (p0) REVERT: A 56 ASP cc_start: 0.7114 (m-30) cc_final: 0.6816 (t0) REVERT: A 246 GLN cc_start: 0.8159 (mt0) cc_final: 0.7954 (mt0) REVERT: A 258 PRO cc_start: 0.8477 (Cg_exo) cc_final: 0.8027 (Cg_endo) REVERT: A 283 MET cc_start: 0.8871 (mmp) cc_final: 0.8643 (mmp) REVERT: A 329 ILE cc_start: 0.8686 (mm) cc_final: 0.8066 (tt) REVERT: A 361 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 41 GLN cc_start: 0.7597 (tp40) cc_final: 0.7334 (tt0) REVERT: B 195 GLU cc_start: 0.8327 (tt0) cc_final: 0.8111 (tt0) REVERT: B 201 VAL cc_start: 0.9003 (m) cc_final: 0.8709 (t) REVERT: B 246 GLN cc_start: 0.7925 (mt0) cc_final: 0.7540 (tt0) REVERT: B 325 MET cc_start: 0.6907 (mmm) cc_final: 0.6436 (mmt) REVERT: B 355 MET cc_start: 0.8224 (mmm) cc_final: 0.7945 (mmt) REVERT: C 201 VAL cc_start: 0.9157 (m) cc_final: 0.8738 (p) REVERT: C 211 ASP cc_start: 0.7538 (t70) cc_final: 0.7290 (m-30) REVERT: C 311 ASP cc_start: 0.7320 (m-30) cc_final: 0.7096 (t0) REVERT: D 149 THR cc_start: 0.8139 (m) cc_final: 0.7922 (t) REVERT: D 287 ILE cc_start: 0.8354 (tt) cc_final: 0.8013 (tt) REVERT: D 349 LEU cc_start: 0.7174 (tp) cc_final: 0.6896 (mt) REVERT: E 56 ASP cc_start: 0.7163 (m-30) cc_final: 0.6787 (t0) REVERT: E 59 GLN cc_start: 0.7852 (mm-40) cc_final: 0.6922 (tp40) REVERT: E 115 ASN cc_start: 0.8438 (t0) cc_final: 0.8181 (t0) REVERT: E 173 HIS cc_start: 0.8406 (p-80) cc_final: 0.8117 (p90) REVERT: E 244 ASP cc_start: 0.7812 (p0) cc_final: 0.7059 (p0) REVERT: E 299 MET cc_start: 0.8328 (mmp) cc_final: 0.8109 (mmt) REVERT: E 371 HIS cc_start: 0.8258 (m-70) cc_final: 0.8039 (m-70) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.2870 time to fit residues: 235.8537 Evaluate side-chains 280 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 145 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS C 41 GLN D 162 ASN D 296 ASN D 360 GLN E 40 HIS E 297 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15245 Z= 0.200 Angle : 0.646 8.040 20705 Z= 0.322 Chirality : 0.046 0.178 2305 Planarity : 0.004 0.032 2630 Dihedral : 11.574 141.022 2175 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.05 % Allowed : 10.41 % Favored : 86.54 % 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 (0.20), residues: 1830 helix: 0.40 (0.18), residues: 825 sheet: 0.20 (0.28), residues: 315 loop : 0.47 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 340 HIS 0.005 0.001 HIS E 371 PHE 0.034 0.001 PHE D 352 TYR 0.019 0.002 TYR D 294 ARG 0.006 0.001 ARG E 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 391 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8338 (mm) cc_final: 0.7922 (pt) REVERT: B 176 MET cc_start: 0.8122 (mmt) cc_final: 0.7302 (mmm) REVERT: B 226 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8014 (mm-30) REVERT: B 246 GLN cc_start: 0.7827 (mt0) cc_final: 0.7427 (tt0) REVERT: C 65 LEU cc_start: 0.8313 (mt) cc_final: 0.8022 (mp) REVERT: C 75 ILE cc_start: 0.8684 (mt) cc_final: 0.8328 (tt) REVERT: C 92 ASN cc_start: 0.8582 (t0) cc_final: 0.8356 (t0) REVERT: C 119 MET cc_start: 0.8416 (ttm) cc_final: 0.8114 (ttm) REVERT: C 201 VAL cc_start: 0.8787 (m) cc_final: 0.8428 (p) REVERT: C 211 ASP cc_start: 0.7661 (t70) cc_final: 0.7175 (m-30) REVERT: C 259 GLU cc_start: 0.7613 (tp30) cc_final: 0.7256 (tp30) REVERT: C 364 GLU cc_start: 0.8757 (tp30) cc_final: 0.8461 (tm-30) REVERT: D 78 ASN cc_start: 0.8071 (t0) cc_final: 0.7449 (m-40) REVERT: D 292 ASP cc_start: 0.7517 (t0) cc_final: 0.7176 (t0) REVERT: E 296 ASN cc_start: 0.8978 (m-40) cc_final: 0.8735 (m-40) outliers start: 48 outliers final: 25 residues processed: 424 average time/residue: 0.2269 time to fit residues: 148.3553 Evaluate side-chains 308 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 283 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN B 111 ASN C 41 GLN C 101 HIS C 360 GLN D 12 ASN D 101 HIS ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15245 Z= 0.287 Angle : 0.665 6.639 20705 Z= 0.326 Chirality : 0.047 0.197 2305 Planarity : 0.005 0.039 2630 Dihedral : 11.170 145.168 2175 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.32 % Allowed : 13.21 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1830 helix: 1.10 (0.19), residues: 730 sheet: 0.34 (0.29), residues: 315 loop : 0.40 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 79 HIS 0.006 0.001 HIS D 161 PHE 0.018 0.002 PHE C 124 TYR 0.021 0.002 TYR D 294 ARG 0.005 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 294 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8365 (mm) cc_final: 0.8123 (pt) REVERT: A 279 TYR cc_start: 0.8507 (t80) cc_final: 0.8170 (t80) REVERT: A 283 MET cc_start: 0.8822 (mmm) cc_final: 0.8563 (mmm) REVERT: B 14 SER cc_start: 0.7775 (t) cc_final: 0.7563 (p) REVERT: B 227 MET cc_start: 0.8672 (mmm) cc_final: 0.8462 (mmm) REVERT: B 311 ASP cc_start: 0.8179 (m-30) cc_final: 0.7831 (m-30) REVERT: B 364 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 82 MET cc_start: 0.9131 (tpt) cc_final: 0.8916 (tpp) REVERT: C 119 MET cc_start: 0.8585 (ttm) cc_final: 0.8361 (ttm) REVERT: C 157 ASP cc_start: 0.8344 (t70) cc_final: 0.8066 (t0) REVERT: C 192 ILE cc_start: 0.8206 (mm) cc_final: 0.8000 (tp) REVERT: C 201 VAL cc_start: 0.8754 (m) cc_final: 0.8374 (p) REVERT: C 211 ASP cc_start: 0.7725 (t70) cc_final: 0.7171 (m-30) REVERT: C 259 GLU cc_start: 0.7736 (tp30) cc_final: 0.7441 (tp30) REVERT: D 311 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: D 326 LYS cc_start: 0.7626 (mmmt) cc_final: 0.7326 (mppt) REVERT: E 222 ASP cc_start: 0.7507 (t0) cc_final: 0.7240 (t0) REVERT: E 271 SER cc_start: 0.8738 (t) cc_final: 0.8380 (m) REVERT: E 298 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8821 (p) REVERT: E 327 ILE cc_start: 0.8597 (mm) cc_final: 0.8110 (tp) outliers start: 68 outliers final: 52 residues processed: 339 average time/residue: 0.2331 time to fit residues: 121.2501 Evaluate side-chains 307 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 253 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 335 ARG Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN B 111 ASN B 353 GLN C 41 GLN C 111 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15245 Z= 0.323 Angle : 0.670 7.280 20705 Z= 0.325 Chirality : 0.047 0.205 2305 Planarity : 0.005 0.044 2630 Dihedral : 11.057 145.711 2175 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.52 % Allowed : 13.97 % Favored : 80.51 % 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: 0.73 (0.19), residues: 1830 helix: 1.13 (0.19), residues: 700 sheet: 0.14 (0.28), residues: 315 loop : 0.20 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.004 0.001 HIS B 88 PHE 0.017 0.002 PHE C 124 TYR 0.020 0.002 TYR D 294 ARG 0.005 0.001 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 291 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8488 (mm) cc_final: 0.8151 (pt) REVERT: A 78 ASN cc_start: 0.7553 (t0) cc_final: 0.7257 (t0) REVERT: A 250 ILE cc_start: 0.8305 (mm) cc_final: 0.8025 (mm) REVERT: A 270 GLU cc_start: 0.5811 (mm-30) cc_final: 0.5554 (mp0) REVERT: A 283 MET cc_start: 0.8707 (mmm) cc_final: 0.8269 (mmm) REVERT: B 116 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7701 (mtm-85) REVERT: B 215 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8532 (mttm) REVERT: B 311 ASP cc_start: 0.8203 (m-30) cc_final: 0.7992 (m-30) REVERT: B 364 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8247 (tm-30) REVERT: C 82 MET cc_start: 0.9137 (tpt) cc_final: 0.8927 (tpp) REVERT: C 119 MET cc_start: 0.8612 (ttm) cc_final: 0.8171 (ttm) REVERT: C 157 ASP cc_start: 0.8664 (t70) cc_final: 0.8424 (t0) REVERT: C 192 ILE cc_start: 0.8040 (mm) cc_final: 0.7454 (pt) REVERT: C 201 VAL cc_start: 0.8707 (m) cc_final: 0.8367 (p) REVERT: C 211 ASP cc_start: 0.7753 (t70) cc_final: 0.7140 (m-30) REVERT: C 217 CYS cc_start: 0.9121 (m) cc_final: 0.8573 (m) REVERT: C 259 GLU cc_start: 0.7811 (tp30) cc_final: 0.7480 (tp30) REVERT: E 271 SER cc_start: 0.8903 (t) cc_final: 0.8530 (m) REVERT: E 298 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9003 (p) REVERT: E 327 ILE cc_start: 0.8605 (mm) cc_final: 0.8353 (tp) outliers start: 87 outliers final: 58 residues processed: 342 average time/residue: 0.2233 time to fit residues: 118.3649 Evaluate side-chains 324 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 264 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 371 HIS C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15245 Z= 0.351 Angle : 0.686 8.166 20705 Z= 0.333 Chirality : 0.048 0.221 2305 Planarity : 0.005 0.041 2630 Dihedral : 11.088 148.311 2175 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.33 % Allowed : 15.17 % Favored : 79.49 % 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: 0.51 (0.19), residues: 1830 helix: 0.98 (0.19), residues: 700 sheet: -0.02 (0.27), residues: 325 loop : 0.08 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.007 0.001 HIS B 101 PHE 0.017 0.002 PHE D 262 TYR 0.019 0.002 TYR A 166 ARG 0.004 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 274 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8565 (mm) cc_final: 0.8279 (pt) REVERT: A 78 ASN cc_start: 0.7643 (t0) cc_final: 0.7305 (t0) REVERT: A 246 GLN cc_start: 0.8027 (mt0) cc_final: 0.7748 (mt0) REVERT: A 270 GLU cc_start: 0.5706 (mm-30) cc_final: 0.5210 (mp0) REVERT: B 116 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7650 (mtm-85) REVERT: B 215 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8475 (mttm) REVERT: B 311 ASP cc_start: 0.8181 (m-30) cc_final: 0.7873 (m-30) REVERT: B 364 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8150 (tm-30) REVERT: C 82 MET cc_start: 0.9101 (tpt) cc_final: 0.8893 (tpp) REVERT: C 119 MET cc_start: 0.8711 (ttm) cc_final: 0.8307 (ttm) REVERT: C 201 VAL cc_start: 0.8776 (m) cc_final: 0.8436 (p) REVERT: C 211 ASP cc_start: 0.7734 (t70) cc_final: 0.7202 (m-30) REVERT: C 259 GLU cc_start: 0.7886 (tp30) cc_final: 0.7524 (tp30) REVERT: D 75 ILE cc_start: 0.8859 (mp) cc_final: 0.8488 (pt) REVERT: D 82 MET cc_start: 0.8740 (tpp) cc_final: 0.8221 (tpt) REVERT: D 326 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7552 (mppt) REVERT: E 283 MET cc_start: 0.7653 (mmp) cc_final: 0.7438 (mmp) REVERT: E 298 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9050 (p) REVERT: E 299 MET cc_start: 0.7825 (mmm) cc_final: 0.7424 (mtt) outliers start: 84 outliers final: 64 residues processed: 326 average time/residue: 0.2177 time to fit residues: 110.6856 Evaluate side-chains 320 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 254 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15245 Z= 0.322 Angle : 0.672 8.269 20705 Z= 0.322 Chirality : 0.047 0.214 2305 Planarity : 0.004 0.038 2630 Dihedral : 11.075 152.833 2175 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.19 % Allowed : 17.21 % Favored : 78.60 % 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: 0.31 (0.19), residues: 1830 helix: 0.83 (0.19), residues: 725 sheet: -0.03 (0.27), residues: 345 loop : -0.13 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 86 HIS 0.007 0.001 HIS B 101 PHE 0.014 0.001 PHE D 262 TYR 0.019 0.002 TYR A 166 ARG 0.003 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 269 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8626 (mm) cc_final: 0.8304 (pt) REVERT: A 78 ASN cc_start: 0.7791 (t0) cc_final: 0.7479 (t0) REVERT: B 215 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8583 (mttm) REVERT: B 311 ASP cc_start: 0.8145 (m-30) cc_final: 0.7835 (m-30) REVERT: B 364 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 119 MET cc_start: 0.8704 (ttm) cc_final: 0.8331 (ttm) REVERT: C 201 VAL cc_start: 0.8709 (m) cc_final: 0.8403 (p) REVERT: C 211 ASP cc_start: 0.7815 (t70) cc_final: 0.7201 (m-30) REVERT: C 259 GLU cc_start: 0.7943 (tp30) cc_final: 0.7579 (tp30) REVERT: D 75 ILE cc_start: 0.8833 (mp) cc_final: 0.8459 (pt) REVERT: E 283 MET cc_start: 0.7719 (mmp) cc_final: 0.7515 (mmp) REVERT: E 298 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9033 (p) REVERT: E 373 LYS cc_start: 0.7293 (mmtt) cc_final: 0.7073 (mttm) outliers start: 66 outliers final: 52 residues processed: 309 average time/residue: 0.2247 time to fit residues: 107.5016 Evaluate side-chains 311 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 257 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15245 Z= 0.183 Angle : 0.608 9.197 20705 Z= 0.286 Chirality : 0.045 0.203 2305 Planarity : 0.004 0.036 2630 Dihedral : 10.605 167.165 2175 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.37 % Allowed : 18.98 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 1830 helix: 1.27 (0.20), residues: 695 sheet: 0.06 (0.27), residues: 345 loop : 0.14 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.005 0.001 HIS B 101 PHE 0.007 0.001 PHE B 255 TYR 0.015 0.001 TYR A 166 ARG 0.005 0.000 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 286 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8220 (t0) REVERT: A 64 ILE cc_start: 0.8603 (mm) cc_final: 0.8367 (pt) REVERT: A 78 ASN cc_start: 0.7756 (t0) cc_final: 0.7254 (m110) REVERT: A 246 GLN cc_start: 0.8015 (mt0) cc_final: 0.7597 (mt0) REVERT: B 167 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7818 (mm-30) REVERT: B 311 ASP cc_start: 0.8105 (m-30) cc_final: 0.7819 (m-30) REVERT: B 364 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 119 MET cc_start: 0.8621 (ttm) cc_final: 0.8270 (ttm) REVERT: C 157 ASP cc_start: 0.8533 (t70) cc_final: 0.8242 (t0) REVERT: C 201 VAL cc_start: 0.8723 (m) cc_final: 0.8397 (p) REVERT: C 217 CYS cc_start: 0.9093 (m) cc_final: 0.8291 (m) REVERT: C 249 THR cc_start: 0.9008 (m) cc_final: 0.8806 (p) REVERT: D 75 ILE cc_start: 0.8693 (mp) cc_final: 0.8387 (pt) REVERT: D 116 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7293 (mtt-85) REVERT: D 313 MET cc_start: 0.7808 (ttm) cc_final: 0.7560 (ttm) outliers start: 53 outliers final: 36 residues processed: 318 average time/residue: 0.2326 time to fit residues: 114.3991 Evaluate side-chains 298 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 260 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 41 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15245 Z= 0.283 Angle : 0.656 8.787 20705 Z= 0.313 Chirality : 0.047 0.210 2305 Planarity : 0.004 0.039 2630 Dihedral : 10.644 170.883 2175 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.49 % Allowed : 19.75 % Favored : 76.76 % 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: 0.54 (0.19), residues: 1830 helix: 1.13 (0.19), residues: 695 sheet: 0.03 (0.27), residues: 345 loop : -0.04 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 86 HIS 0.007 0.001 HIS B 101 PHE 0.012 0.001 PHE D 262 TYR 0.018 0.001 TYR A 166 ARG 0.003 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 267 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8684 (mm) cc_final: 0.8432 (pt) REVERT: A 78 ASN cc_start: 0.7781 (t0) cc_final: 0.7454 (t0) REVERT: A 246 GLN cc_start: 0.8004 (mt0) cc_final: 0.7420 (mt0) REVERT: A 279 TYR cc_start: 0.8564 (t80) cc_final: 0.8178 (t80) REVERT: B 215 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8532 (mttm) REVERT: B 311 ASP cc_start: 0.8167 (m-30) cc_final: 0.7883 (m-30) REVERT: B 364 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 119 MET cc_start: 0.8625 (ttm) cc_final: 0.8309 (ttm) REVERT: C 201 VAL cc_start: 0.8705 (m) cc_final: 0.8396 (p) REVERT: C 292 ASP cc_start: 0.8049 (t0) cc_final: 0.7314 (t0) REVERT: D 75 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8408 (pt) REVERT: D 116 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7457 (mtt-85) outliers start: 55 outliers final: 44 residues processed: 303 average time/residue: 0.2272 time to fit residues: 106.2232 Evaluate side-chains 299 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 157 optimal weight: 0.0570 chunk 165 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15245 Z= 0.295 Angle : 0.671 9.754 20705 Z= 0.320 Chirality : 0.047 0.213 2305 Planarity : 0.004 0.039 2630 Dihedral : 10.211 130.800 2175 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.68 % Allowed : 20.06 % Favored : 76.25 % 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: 0.43 (0.19), residues: 1830 helix: 1.04 (0.19), residues: 695 sheet: -0.01 (0.27), residues: 345 loop : -0.13 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 340 HIS 0.007 0.001 HIS B 101 PHE 0.014 0.001 PHE D 262 TYR 0.017 0.001 TYR A 166 ARG 0.003 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 261 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5672 (pmm) cc_final: 0.5050 (ptt) REVERT: A 64 ILE cc_start: 0.8644 (mm) cc_final: 0.8402 (pt) REVERT: A 78 ASN cc_start: 0.7850 (t0) cc_final: 0.7329 (m110) REVERT: A 246 GLN cc_start: 0.8008 (mt0) cc_final: 0.7483 (mt0) REVERT: A 270 GLU cc_start: 0.5710 (mm-30) cc_final: 0.5432 (mm-30) REVERT: B 215 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8589 (mttm) REVERT: B 311 ASP cc_start: 0.8214 (m-30) cc_final: 0.7940 (m-30) REVERT: B 364 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 119 MET cc_start: 0.8673 (ttm) cc_final: 0.8361 (ttm) REVERT: C 201 VAL cc_start: 0.8693 (m) cc_final: 0.8444 (p) REVERT: C 292 ASP cc_start: 0.8047 (t0) cc_final: 0.7317 (t0) REVERT: D 75 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8389 (pt) REVERT: D 116 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7408 (mtt-85) REVERT: D 132 MET cc_start: 0.8854 (ppp) cc_final: 0.8566 (tmm) outliers start: 58 outliers final: 50 residues processed: 298 average time/residue: 0.2268 time to fit residues: 104.5809 Evaluate side-chains 302 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 249 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15245 Z= 0.206 Angle : 0.634 13.450 20705 Z= 0.299 Chirality : 0.045 0.198 2305 Planarity : 0.004 0.037 2630 Dihedral : 9.775 127.582 2175 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.11 % Allowed : 20.95 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1830 helix: 1.14 (0.20), residues: 695 sheet: 0.01 (0.27), residues: 345 loop : -0.04 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.006 0.001 HIS B 101 PHE 0.010 0.001 PHE A 31 TYR 0.017 0.001 TYR A 166 ARG 0.004 0.000 ARG E 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 270 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8684 (mm) cc_final: 0.8469 (pt) REVERT: A 78 ASN cc_start: 0.7851 (t0) cc_final: 0.7296 (m110) REVERT: A 246 GLN cc_start: 0.7949 (mt0) cc_final: 0.7543 (mt0) REVERT: B 215 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8645 (mttm) REVERT: B 311 ASP cc_start: 0.8140 (m-30) cc_final: 0.7776 (m-30) REVERT: B 364 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8092 (tm-30) REVERT: C 157 ASP cc_start: 0.8486 (t70) cc_final: 0.8238 (t0) REVERT: C 201 VAL cc_start: 0.8691 (m) cc_final: 0.8431 (p) REVERT: C 249 THR cc_start: 0.9007 (m) cc_final: 0.8779 (p) REVERT: C 292 ASP cc_start: 0.8003 (t0) cc_final: 0.7301 (t0) REVERT: D 75 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8383 (pt) REVERT: D 132 MET cc_start: 0.8859 (ppp) cc_final: 0.8550 (tmm) REVERT: D 157 ASP cc_start: 0.6672 (t70) cc_final: 0.6427 (t0) outliers start: 49 outliers final: 40 residues processed: 300 average time/residue: 0.2291 time to fit residues: 106.4097 Evaluate side-chains 299 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 257 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.091009 restraints weight = 24432.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.093834 restraints weight = 14087.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095820 restraints weight = 9210.373| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15245 Z= 0.480 Angle : 0.799 10.299 20705 Z= 0.388 Chirality : 0.052 0.224 2305 Planarity : 0.005 0.049 2630 Dihedral : 10.524 133.184 2175 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.62 % Allowed : 20.83 % Favored : 75.56 % 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: -0.06 (0.19), residues: 1830 helix: 0.61 (0.19), residues: 695 sheet: -0.21 (0.27), residues: 345 loop : -0.42 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 340 HIS 0.009 0.001 HIS B 101 PHE 0.020 0.002 PHE D 262 TYR 0.019 0.002 TYR A 166 ARG 0.006 0.001 ARG D 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.60 seconds wall clock time: 55 minutes 39.23 seconds (3339.23 seconds total)