Starting phenix.real_space_refine on Sat Mar 16 12:27:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t25_10367/03_2024/6t25_10367_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t25_10367/03_2024/6t25_10367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t25_10367/03_2024/6t25_10367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t25_10367/03_2024/6t25_10367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t25_10367/03_2024/6t25_10367_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t25_10367/03_2024/6t25_10367_updated.pdb" } resolution = 3.6 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 95 5.16 5 C 9200 2.51 5 N 2460 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" 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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 241": "OE1" <-> "OE2" 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 "A ARG 372": "NH1" <-> "NH2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" 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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" 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 "B ARG 372": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" 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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 241": "OE1" <-> "OE2" 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 "C ARG 372": "NH1" <-> "NH2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" 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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 241": "OE1" <-> "OE2" 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 "D ARG 372": "NH1" <-> "NH2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 72": "OE1" <-> "OE2" 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 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 241": "OE1" <-> "OE2" 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" Residue "E ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14590 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2835 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2835 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2835 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2835 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2835 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 7.64, per 1000 atoms: 0.52 Number of scatterers: 14590 At special positions: 0 Unit cell: (96.32, 92.96, 188.16, 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 95 16.00 P 10 15.00 Mg 5 11.99 O 2820 8.00 N 2460 7.00 C 9200 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: 6.13 Conformation dependent library (CDL) restraints added in 2.7 seconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 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: 3420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 20 sheets defined 45.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 56 through 64 removed outlier: 5.603A pdb=" N GLY A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 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 123 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.526A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.990A pdb=" N LYS A 291 " --> 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: 5.233A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.637A 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 370 Processing helix chain 'B' and resid 56 through 64 removed outlier: 5.603A pdb=" N GLY B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 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 123 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.526A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.990A pdb=" N LYS B 291 " --> 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: 5.233A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.638A 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 370 Processing helix chain 'C' and resid 56 through 64 removed outlier: 5.602A pdb=" N GLY C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 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 123 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.527A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.990A pdb=" N LYS C 291 " --> 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: 5.233A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.637A 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 370 Processing helix chain 'D' and resid 56 through 64 removed outlier: 5.603A pdb=" N GLY D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 92 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 123 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.526A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.990A pdb=" N LYS D 291 " --> 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: 5.232A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.637A 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 370 Processing helix chain 'E' and resid 56 through 64 removed outlier: 5.602A pdb=" N GLY E 63 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 92 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 123 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.527A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.990A pdb=" N LYS E 291 " --> 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: 5.232A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.637A 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 370 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.700A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 65 through 69 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.999A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.700A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 65 through 69 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 5.999A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.700A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 5.999A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.700A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 65 through 69 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 5.999A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.700A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 65 through 69 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 5.999A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 580 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 6.57 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: 3601 1.32 - 1.44: 3591 1.44 - 1.57: 7553 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 14910 Sorted by residual: bond pdb=" CA EEP F 2 " pdb=" C EEP F 2 " ideal model delta sigma weight residual 1.572 1.480 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.480 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" CA ILE E 192 " pdb=" CB ILE E 192 " ideal model delta sigma weight residual 1.540 1.480 0.059 1.29e-02 6.01e+03 2.12e+01 bond pdb=" CA EEP G 2 " pdb=" C EEP G 2 " ideal model delta sigma weight residual 1.572 1.480 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.480 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 14905 not shown) Histogram of bond angle deviations from ideal: 98.43 - 106.07: 547 106.07 - 113.70: 8446 113.70 - 121.34: 7939 121.34 - 128.97: 3213 128.97 - 136.60: 110 Bond angle restraints: 20255 Sorted by residual: angle pdb=" C GLY B 366 " pdb=" N PRO B 367 " pdb=" CA PRO B 367 " ideal model delta sigma weight residual 119.47 129.65 -10.18 1.16e+00 7.43e-01 7.70e+01 angle pdb=" C GLY C 366 " pdb=" N PRO C 367 " pdb=" CA PRO C 367 " ideal model delta sigma weight residual 119.47 129.64 -10.17 1.16e+00 7.43e-01 7.69e+01 angle pdb=" C GLY D 366 " pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 119.47 129.63 -10.16 1.16e+00 7.43e-01 7.67e+01 angle pdb=" C GLY E 366 " pdb=" N PRO E 367 " pdb=" CA PRO E 367 " ideal model delta sigma weight residual 119.47 129.60 -10.13 1.16e+00 7.43e-01 7.62e+01 angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.47 129.59 -10.12 1.16e+00 7.43e-01 7.61e+01 ... (remaining 20250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.11: 8810 30.11 - 60.21: 110 60.21 - 90.32: 30 90.32 - 120.42: 0 120.42 - 150.53: 10 Dihedral angle restraints: 8960 sinusoidal: 3630 harmonic: 5330 Sorted by residual: dihedral pdb=" O1B ADP E 376 " pdb=" O3A ADP E 376 " pdb=" PB ADP E 376 " pdb=" PA ADP E 376 " ideal model delta sinusoidal sigma weight residual -60.00 90.53 -150.53 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" O1B ADP D 376 " pdb=" O3A ADP D 376 " pdb=" PB ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sinusoidal sigma weight residual -60.00 90.49 -150.49 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" O1B ADP A 376 " pdb=" O3A ADP A 376 " pdb=" PB ADP A 376 " pdb=" PA ADP A 376 " ideal model delta sinusoidal sigma weight residual -60.00 90.47 -150.48 1 2.00e+01 2.50e-03 4.49e+01 ... (remaining 8957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 815 0.048 - 0.097: 761 0.097 - 0.145: 478 0.145 - 0.194: 161 0.194 - 0.242: 45 Chirality restraints: 2260 Sorted by residual: chirality pdb=" CA LYS D 113 " pdb=" N LYS D 113 " pdb=" C LYS D 113 " pdb=" CB LYS D 113 " 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 LYS E 113 " pdb=" N LYS E 113 " pdb=" C LYS E 113 " pdb=" CB LYS E 113 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LYS B 113 " pdb=" N LYS B 113 " pdb=" C LYS B 113 " pdb=" CB LYS B 113 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2257 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " 0.030 2.00e-02 2.50e+03 1.52e-02 5.75e+00 pdb=" CG TRP B 340 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 69 " 0.032 2.00e-02 2.50e+03 1.69e-02 5.74e+00 pdb=" CG TYR A 69 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 69 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 69 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 69 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 69 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 69 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 69 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 69 " 0.031 2.00e-02 2.50e+03 1.69e-02 5.71e+00 pdb=" CG TYR C 69 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR C 69 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 69 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 69 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 69 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 69 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 69 " 0.025 2.00e-02 2.50e+03 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 15 2.05 - 2.76: 3307 2.76 - 3.47: 20708 3.47 - 4.19: 36682 4.19 - 4.90: 62543 Nonbonded interactions: 123255 Sorted by model distance: nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.335 3.350 nonbonded pdb=" N TRP G 1 " pdb=" C ALA G 7 " model vdw 1.336 3.350 nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.336 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.336 3.350 nonbonded pdb=" N TRP F 1 " pdb=" C ALA F 7 " model vdw 1.337 3.350 ... (remaining 123250 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: 0.980 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: 4.130 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 40.540 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.018 0.092 14910 Z= 1.197 Angle : 1.593 10.178 20255 Z= 1.066 Chirality : 0.089 0.242 2260 Planarity : 0.006 0.046 2570 Dihedral : 12.247 150.531 5540 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.32 % Allowed : 0.00 % Favored : 99.68 % 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: -0.96 (0.18), residues: 1775 helix: -0.97 (0.16), residues: 820 sheet: -0.76 (0.26), residues: 320 loop : 0.32 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.008 TRP B 340 HIS 0.006 0.002 HIS D 161 PHE 0.011 0.003 PHE B 262 TYR 0.032 0.006 TYR A 69 ARG 0.006 0.001 ARG E 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 512 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASN cc_start: 0.8253 (m-40) cc_final: 0.8001 (t0) REVERT: A 316 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8123 (mm-30) REVERT: A 372 ARG cc_start: 0.6226 (ttp-170) cc_final: 0.5971 (ttp-170) REVERT: B 34 ILE cc_start: 0.8755 (mt) cc_final: 0.8506 (pt) REVERT: B 59 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6824 (mm-40) REVERT: B 151 ILE cc_start: 0.8592 (mt) cc_final: 0.8257 (tt) REVERT: B 202 THR cc_start: 0.7519 (p) cc_final: 0.6804 (p) REVERT: B 325 MET cc_start: 0.7814 (mmm) cc_final: 0.7464 (mmt) REVERT: C 143 TYR cc_start: 0.8430 (m-80) cc_final: 0.8117 (m-10) REVERT: C 157 ASP cc_start: 0.8311 (t70) cc_final: 0.7793 (t70) REVERT: C 227 MET cc_start: 0.8113 (mmm) cc_final: 0.7720 (tpp) REVERT: D 11 ASP cc_start: 0.8202 (t0) cc_final: 0.7945 (t0) REVERT: D 117 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7335 (tm-30) REVERT: D 202 THR cc_start: 0.7912 (p) cc_final: 0.7085 (p) REVERT: D 222 ASP cc_start: 0.8283 (t0) cc_final: 0.7517 (p0) REVERT: D 324 THR cc_start: 0.8293 (p) cc_final: 0.8026 (p) REVERT: E 34 ILE cc_start: 0.9196 (mt) cc_final: 0.8907 (pt) REVERT: E 78 ASN cc_start: 0.7580 (t0) cc_final: 0.6963 (m-40) REVERT: E 93 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6380 (mm-30) REVERT: G 5 CYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6274 (p) outliers start: 5 outliers final: 0 residues processed: 517 average time/residue: 0.2647 time to fit residues: 197.1403 Evaluate side-chains 235 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 92 ASN D 173 HIS D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14910 Z= 0.208 Angle : 0.648 6.719 20255 Z= 0.313 Chirality : 0.047 0.212 2260 Planarity : 0.004 0.031 2570 Dihedral : 11.956 150.660 2121 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.34 % Allowed : 9.55 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1775 helix: 0.88 (0.18), residues: 740 sheet: -0.41 (0.25), residues: 345 loop : 1.61 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.008 0.001 HIS B 173 PHE 0.009 0.001 PHE A 352 TYR 0.018 0.001 TYR B 188 ARG 0.005 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 328 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.6667 (mptt) REVERT: A 176 MET cc_start: 0.7590 (mmp) cc_final: 0.6956 (mmt) REVERT: A 325 MET cc_start: 0.7269 (mmp) cc_final: 0.6650 (mmt) REVERT: B 83 GLU cc_start: 0.7939 (tt0) cc_final: 0.7587 (tm-30) REVERT: B 142 LEU cc_start: 0.8607 (tp) cc_final: 0.8398 (tp) REVERT: B 191 LYS cc_start: 0.8053 (mttt) cc_final: 0.7825 (mtpt) REVERT: C 57 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7346 (mt-10) REVERT: C 143 TYR cc_start: 0.8076 (m-80) cc_final: 0.7790 (m-10) REVERT: C 157 ASP cc_start: 0.8399 (t70) cc_final: 0.7779 (t70) REVERT: C 313 MET cc_start: 0.8040 (tpp) cc_final: 0.7737 (tpp) REVERT: D 57 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7256 (mt-10) REVERT: D 117 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7116 (tm-30) REVERT: D 140 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8540 (mt) REVERT: D 143 TYR cc_start: 0.7775 (m-80) cc_final: 0.7242 (m-80) REVERT: D 162 ASN cc_start: 0.8006 (t0) cc_final: 0.7762 (t0) REVERT: D 222 ASP cc_start: 0.8026 (t0) cc_final: 0.7588 (p0) REVERT: D 283 MET cc_start: 0.7875 (mmp) cc_final: 0.7472 (mmm) REVERT: E 93 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6494 (mm-30) REVERT: E 238 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8243 (mtpt) REVERT: E 311 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: E 316 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7978 (mm-30) REVERT: E 363 ASP cc_start: 0.6972 (t0) cc_final: 0.5790 (p0) outliers start: 36 outliers final: 19 residues processed: 356 average time/residue: 0.2378 time to fit residues: 128.0402 Evaluate side-chains 267 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 311 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 0.0010 chunk 162 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 0.2980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN D 88 HIS D 263 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14910 Z= 0.158 Angle : 0.573 6.848 20255 Z= 0.271 Chirality : 0.044 0.195 2260 Planarity : 0.004 0.032 2570 Dihedral : 11.357 149.362 2120 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.47 % Allowed : 12.92 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1775 helix: 1.24 (0.19), residues: 745 sheet: -0.19 (0.26), residues: 345 loop : 1.88 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.008 0.001 HIS B 173 PHE 0.008 0.001 PHE E 127 TYR 0.010 0.001 TYR E 53 ARG 0.005 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 284 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7053 (mptt) REVERT: A 117 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7851 (mp0) REVERT: A 176 MET cc_start: 0.7520 (mmp) cc_final: 0.6834 (mmt) REVERT: A 325 MET cc_start: 0.7575 (mmp) cc_final: 0.7261 (tpp) REVERT: A 355 MET cc_start: 0.7881 (mtt) cc_final: 0.7575 (mtt) REVERT: B 81 ASP cc_start: 0.7151 (m-30) cc_final: 0.6935 (m-30) REVERT: B 83 GLU cc_start: 0.7891 (tt0) cc_final: 0.7498 (tm-30) REVERT: B 142 LEU cc_start: 0.8649 (tp) cc_final: 0.8426 (tp) REVERT: B 191 LYS cc_start: 0.8161 (mttt) cc_final: 0.7909 (mtpt) REVERT: C 57 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7447 (mt-10) REVERT: C 121 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8312 (tm-30) REVERT: C 143 TYR cc_start: 0.8158 (m-80) cc_final: 0.7841 (m-10) REVERT: C 157 ASP cc_start: 0.8330 (t70) cc_final: 0.7739 (t70) REVERT: C 313 MET cc_start: 0.8028 (tpp) cc_final: 0.7709 (tpp) REVERT: C 328 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8185 (ttmm) REVERT: D 88 HIS cc_start: 0.7852 (t70) cc_final: 0.7419 (t70) REVERT: D 117 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7043 (tm-30) REVERT: D 140 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8610 (mt) REVERT: D 143 TYR cc_start: 0.7696 (m-80) cc_final: 0.7214 (m-80) REVERT: D 162 ASN cc_start: 0.8072 (t0) cc_final: 0.7720 (t0) REVERT: D 222 ASP cc_start: 0.7910 (t0) cc_final: 0.7317 (p0) REVERT: D 227 MET cc_start: 0.7383 (mmm) cc_final: 0.7156 (mmm) REVERT: D 283 MET cc_start: 0.7844 (mmp) cc_final: 0.7511 (mmm) REVERT: D 334 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: E 84 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7959 (tptt) REVERT: E 93 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6473 (mm-30) REVERT: E 189 LEU cc_start: 0.8864 (tp) cc_final: 0.8536 (tp) REVERT: E 217 CYS cc_start: 0.8091 (OUTLIER) cc_final: 0.6879 (m) REVERT: E 225 ASN cc_start: 0.8475 (m110) cc_final: 0.8078 (m110) REVERT: E 238 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8113 (mtpt) REVERT: E 313 MET cc_start: 0.8616 (tpp) cc_final: 0.8369 (tpp) REVERT: E 316 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8022 (mm-30) REVERT: E 372 ARG cc_start: 0.5382 (mtp180) cc_final: 0.5119 (mtp180) outliers start: 38 outliers final: 17 residues processed: 311 average time/residue: 0.2306 time to fit residues: 109.5517 Evaluate side-chains 249 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 12 ASN B 40 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14910 Z= 0.384 Angle : 0.700 9.251 20255 Z= 0.336 Chirality : 0.049 0.264 2260 Planarity : 0.005 0.037 2570 Dihedral : 11.528 157.038 2120 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.51 % Allowed : 14.16 % Favored : 82.34 % 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: 0.94 (0.20), residues: 1775 helix: 0.74 (0.19), residues: 745 sheet: -0.44 (0.25), residues: 345 loop : 1.44 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 86 HIS 0.005 0.001 HIS D 101 PHE 0.014 0.002 PHE D 124 TYR 0.015 0.002 TYR C 198 ARG 0.004 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 261 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7293 (mptt) REVERT: A 117 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 176 MET cc_start: 0.7436 (mmp) cc_final: 0.6972 (mmt) REVERT: A 325 MET cc_start: 0.8065 (mmp) cc_final: 0.7645 (mmt) REVERT: B 57 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7805 (mp0) REVERT: B 83 GLU cc_start: 0.8151 (tt0) cc_final: 0.7761 (tm-30) REVERT: B 334 GLU cc_start: 0.8447 (mp0) cc_final: 0.7750 (pp20) REVERT: C 49 GLN cc_start: 0.6651 (mt0) cc_final: 0.6434 (mt0) REVERT: C 57 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7546 (mt-10) REVERT: C 121 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8292 (tm-30) REVERT: C 143 TYR cc_start: 0.8016 (m-80) cc_final: 0.7651 (m-10) REVERT: C 157 ASP cc_start: 0.8439 (t70) cc_final: 0.7921 (t70) REVERT: D 88 HIS cc_start: 0.7913 (t70) cc_final: 0.7551 (t70) REVERT: D 121 GLN cc_start: 0.8527 (tt0) cc_final: 0.8314 (tt0) REVERT: D 140 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8770 (mt) REVERT: D 143 TYR cc_start: 0.7880 (m-80) cc_final: 0.7539 (m-80) REVERT: D 176 MET cc_start: 0.7689 (mmp) cc_final: 0.7397 (mmt) REVERT: D 324 THR cc_start: 0.7498 (p) cc_final: 0.7297 (p) REVERT: D 325 MET cc_start: 0.8017 (mmm) cc_final: 0.7745 (mmm) REVERT: D 334 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: E 93 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6368 (mm-30) REVERT: E 125 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7290 (mm-30) REVERT: E 316 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8006 (mm-30) REVERT: E 372 ARG cc_start: 0.5523 (mtp180) cc_final: 0.5275 (mtm-85) outliers start: 54 outliers final: 37 residues processed: 304 average time/residue: 0.2558 time to fit residues: 115.6001 Evaluate side-chains 257 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 88 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14910 Z= 0.214 Angle : 0.595 7.716 20255 Z= 0.278 Chirality : 0.046 0.223 2260 Planarity : 0.004 0.035 2570 Dihedral : 10.933 158.296 2120 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.79 % Allowed : 16.23 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1775 helix: 0.82 (0.19), residues: 745 sheet: -0.39 (0.26), residues: 345 loop : 1.44 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.005 0.001 HIS A 101 PHE 0.007 0.001 PHE D 255 TYR 0.010 0.001 TYR C 198 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 256 time to evaluate : 1.577 Fit side-chains REVERT: A 113 LYS cc_start: 0.8344 (mttm) cc_final: 0.7152 (mptt) REVERT: A 117 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7536 (mp0) REVERT: A 176 MET cc_start: 0.7538 (mmp) cc_final: 0.7145 (mmt) REVERT: A 192 ILE cc_start: 0.8936 (mm) cc_final: 0.8610 (mm) REVERT: A 325 MET cc_start: 0.8420 (mmp) cc_final: 0.7968 (mmt) REVERT: B 57 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7760 (mp0) REVERT: B 83 GLU cc_start: 0.8048 (tt0) cc_final: 0.7674 (tm-30) REVERT: B 143 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7357 (t80) REVERT: B 162 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7910 (t0) REVERT: C 57 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7695 (mt-10) REVERT: C 95 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8684 (ttm-80) REVERT: C 121 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 143 TYR cc_start: 0.7934 (m-80) cc_final: 0.7531 (m-10) REVERT: C 313 MET cc_start: 0.8112 (tpp) cc_final: 0.7795 (tpp) REVERT: D 88 HIS cc_start: 0.7874 (t70) cc_final: 0.7550 (t70) REVERT: D 121 GLN cc_start: 0.8452 (tt0) cc_final: 0.8232 (tt0) REVERT: D 140 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8757 (mt) REVERT: D 143 TYR cc_start: 0.7689 (m-80) cc_final: 0.7360 (m-80) REVERT: D 162 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7951 (t0) REVERT: D 176 MET cc_start: 0.7786 (mmp) cc_final: 0.7569 (mmt) REVERT: D 324 THR cc_start: 0.7377 (p) cc_final: 0.7152 (p) REVERT: D 334 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: E 93 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6279 (mm-30) REVERT: E 121 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 316 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7970 (mm-30) outliers start: 43 outliers final: 28 residues processed: 289 average time/residue: 0.2324 time to fit residues: 101.5858 Evaluate side-chains 257 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 0.0050 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14910 Z= 0.215 Angle : 0.592 8.047 20255 Z= 0.276 Chirality : 0.045 0.221 2260 Planarity : 0.004 0.035 2570 Dihedral : 10.665 163.733 2120 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.99 % Allowed : 17.27 % Favored : 79.74 % 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: 0.98 (0.20), residues: 1775 helix: 0.80 (0.19), residues: 745 sheet: -0.32 (0.27), residues: 345 loop : 1.35 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE D 352 TYR 0.009 0.001 TYR E 69 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 1.456 Fit side-chains REVERT: A 101 HIS cc_start: 0.8258 (m-70) cc_final: 0.8035 (m-70) REVERT: A 113 LYS cc_start: 0.8442 (mttm) cc_final: 0.7302 (mptt) REVERT: A 117 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7436 (mp0) REVERT: A 176 MET cc_start: 0.7536 (mmp) cc_final: 0.7155 (mmt) REVERT: A 325 MET cc_start: 0.8500 (mmp) cc_final: 0.8099 (mmt) REVERT: B 57 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7785 (mp0) REVERT: B 83 GLU cc_start: 0.8073 (tt0) cc_final: 0.7703 (tm-30) REVERT: B 143 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7323 (t80) REVERT: B 162 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7821 (t0) REVERT: C 57 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7710 (mt-10) REVERT: C 95 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8686 (ttm-80) REVERT: C 121 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 143 TYR cc_start: 0.7906 (m-80) cc_final: 0.7529 (m-10) REVERT: D 88 HIS cc_start: 0.7802 (t70) cc_final: 0.7538 (t70) REVERT: D 121 GLN cc_start: 0.8449 (tt0) cc_final: 0.8241 (tt0) REVERT: D 123 MET cc_start: 0.8427 (tpp) cc_final: 0.8131 (tpt) REVERT: D 140 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8673 (mt) REVERT: D 143 TYR cc_start: 0.7709 (m-80) cc_final: 0.7403 (m-80) REVERT: D 162 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7970 (t0) REVERT: D 176 MET cc_start: 0.7765 (mmp) cc_final: 0.7510 (mmt) REVERT: D 313 MET cc_start: 0.8094 (ttm) cc_final: 0.7877 (ttm) REVERT: D 334 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: E 57 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7770 (mp0) REVERT: E 93 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6246 (mm-30) REVERT: E 121 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8470 (tm-30) REVERT: E 224 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7652 (tm-30) REVERT: E 316 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7914 (mm-30) outliers start: 46 outliers final: 33 residues processed: 276 average time/residue: 0.2255 time to fit residues: 95.9796 Evaluate side-chains 259 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 173 optimal weight: 0.0770 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14910 Z= 0.149 Angle : 0.568 9.750 20255 Z= 0.261 Chirality : 0.044 0.210 2260 Planarity : 0.004 0.034 2570 Dihedral : 10.185 175.659 2120 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.60 % Allowed : 18.31 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1775 helix: 0.94 (0.19), residues: 740 sheet: -0.28 (0.27), residues: 345 loop : 1.42 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.005 0.001 HIS A 371 PHE 0.007 0.001 PHE D 352 TYR 0.007 0.001 TYR E 306 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 264 time to evaluate : 1.724 Fit side-chains REVERT: A 113 LYS cc_start: 0.8380 (mttm) cc_final: 0.7159 (mptt) REVERT: A 117 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7231 (mp0) REVERT: A 176 MET cc_start: 0.7543 (mmp) cc_final: 0.7182 (mmt) REVERT: A 325 MET cc_start: 0.8458 (mmp) cc_final: 0.8077 (mmt) REVERT: A 345 ILE cc_start: 0.9392 (mm) cc_final: 0.9157 (mt) REVERT: B 51 ASP cc_start: 0.8068 (m-30) cc_final: 0.7707 (t70) REVERT: B 83 GLU cc_start: 0.8000 (tt0) cc_final: 0.7662 (tm-30) REVERT: B 143 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7210 (t80) REVERT: B 162 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7708 (t0) REVERT: C 57 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7676 (mt-10) REVERT: C 95 ARG cc_start: 0.8867 (mmm-85) cc_final: 0.8638 (ttm-80) REVERT: C 121 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 143 TYR cc_start: 0.7894 (m-80) cc_final: 0.7569 (m-10) REVERT: D 84 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7903 (mtmt) REVERT: D 88 HIS cc_start: 0.7800 (t70) cc_final: 0.7548 (t70) REVERT: D 123 MET cc_start: 0.8360 (tpp) cc_final: 0.8027 (tpt) REVERT: D 140 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8631 (mt) REVERT: D 143 TYR cc_start: 0.7633 (m-80) cc_final: 0.7336 (m-80) REVERT: D 162 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7981 (t0) REVERT: D 313 MET cc_start: 0.7985 (ttm) cc_final: 0.7776 (ttm) REVERT: D 334 GLU cc_start: 0.7850 (mp0) cc_final: 0.7373 (tm-30) REVERT: E 57 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7821 (mp0) REVERT: E 93 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6267 (mm-30) REVERT: E 121 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8234 (tm-30) REVERT: E 123 MET cc_start: 0.8192 (tpp) cc_final: 0.7562 (tpt) REVERT: E 244 ASP cc_start: 0.7517 (p0) cc_final: 0.6971 (t0) outliers start: 40 outliers final: 25 residues processed: 291 average time/residue: 0.2268 time to fit residues: 101.1852 Evaluate side-chains 263 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14910 Z= 0.379 Angle : 0.683 9.610 20255 Z= 0.324 Chirality : 0.049 0.238 2260 Planarity : 0.005 0.035 2570 Dihedral : 10.368 171.424 2120 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.51 % Allowed : 18.38 % Favored : 78.12 % 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: 0.64 (0.20), residues: 1775 helix: 0.59 (0.19), residues: 740 sheet: -0.50 (0.27), residues: 345 loop : 1.07 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.008 0.001 HIS B 161 PHE 0.011 0.002 PHE D 124 TYR 0.015 0.002 TYR C 198 ARG 0.005 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 230 time to evaluate : 1.779 Fit side-chains REVERT: A 101 HIS cc_start: 0.8253 (m-70) cc_final: 0.8026 (m-70) REVERT: A 113 LYS cc_start: 0.8411 (mttm) cc_final: 0.7163 (mptt) REVERT: A 117 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7538 (mp0) REVERT: A 176 MET cc_start: 0.7578 (mmp) cc_final: 0.7235 (mmt) REVERT: A 325 MET cc_start: 0.8521 (mmp) cc_final: 0.8201 (mmt) REVERT: B 51 ASP cc_start: 0.8139 (m-30) cc_final: 0.7876 (t0) REVERT: B 83 GLU cc_start: 0.8194 (tt0) cc_final: 0.7787 (tm-30) REVERT: B 143 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7267 (t80) REVERT: B 162 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8002 (t0) REVERT: C 57 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7599 (mt-10) REVERT: C 95 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8638 (ttm-80) REVERT: C 121 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8210 (tm-30) REVERT: C 143 TYR cc_start: 0.7927 (m-80) cc_final: 0.7589 (m-10) REVERT: C 157 ASP cc_start: 0.8467 (t70) cc_final: 0.7953 (t70) REVERT: D 88 HIS cc_start: 0.7863 (t70) cc_final: 0.7615 (t70) REVERT: D 123 MET cc_start: 0.8382 (tpp) cc_final: 0.8050 (tpt) REVERT: D 140 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8755 (mt) REVERT: D 143 TYR cc_start: 0.7849 (m-80) cc_final: 0.7579 (m-80) REVERT: D 313 MET cc_start: 0.8145 (ttm) cc_final: 0.7920 (ttm) REVERT: D 334 GLU cc_start: 0.7974 (mp0) cc_final: 0.7443 (tm-30) REVERT: E 57 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7887 (mp0) REVERT: E 96 VAL cc_start: 0.8373 (p) cc_final: 0.8043 (m) REVERT: E 121 GLN cc_start: 0.8701 (tm-30) cc_final: 0.7997 (tm-30) REVERT: E 244 ASP cc_start: 0.7566 (p0) cc_final: 0.7227 (t0) outliers start: 54 outliers final: 43 residues processed: 268 average time/residue: 0.2310 time to fit residues: 94.6204 Evaluate side-chains 269 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 271 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 152 optimal weight: 0.0470 chunk 106 optimal weight: 3.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN D 162 ASN E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14910 Z= 0.173 Angle : 0.596 9.494 20255 Z= 0.274 Chirality : 0.045 0.217 2260 Planarity : 0.004 0.034 2570 Dihedral : 9.232 116.667 2120 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.88 % Allowed : 20.26 % Favored : 77.86 % 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: 0.88 (0.20), residues: 1775 helix: 0.80 (0.19), residues: 740 sheet: -0.39 (0.27), residues: 345 loop : 1.19 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.005 0.001 HIS A 371 PHE 0.008 0.001 PHE D 352 TYR 0.026 0.001 TYR C 294 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 241 time to evaluate : 1.630 Fit side-chains REVERT: A 101 HIS cc_start: 0.8226 (m-70) cc_final: 0.8014 (m-70) REVERT: A 113 LYS cc_start: 0.8458 (mttm) cc_final: 0.7167 (mptt) REVERT: A 117 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7298 (mp0) REVERT: A 176 MET cc_start: 0.7524 (mmp) cc_final: 0.7169 (mmt) REVERT: A 325 MET cc_start: 0.8444 (mmp) cc_final: 0.8159 (mmt) REVERT: B 51 ASP cc_start: 0.8155 (m-30) cc_final: 0.7846 (t0) REVERT: B 83 GLU cc_start: 0.8181 (tt0) cc_final: 0.7860 (tm-30) REVERT: B 143 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7286 (t80) REVERT: B 162 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7874 (t0) REVERT: C 57 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7586 (mt-10) REVERT: C 95 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8669 (ttm-80) REVERT: C 143 TYR cc_start: 0.7846 (m-80) cc_final: 0.7532 (m-10) REVERT: C 313 MET cc_start: 0.8127 (tpp) cc_final: 0.7831 (tpp) REVERT: C 334 GLU cc_start: 0.8567 (pt0) cc_final: 0.8096 (pp20) REVERT: D 88 HIS cc_start: 0.7813 (t70) cc_final: 0.7566 (t70) REVERT: D 123 MET cc_start: 0.8306 (tpp) cc_final: 0.7982 (tpt) REVERT: D 140 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8683 (mt) REVERT: D 143 TYR cc_start: 0.7655 (m-80) cc_final: 0.7388 (m-80) REVERT: D 162 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7908 (t0) REVERT: D 313 MET cc_start: 0.7986 (ttm) cc_final: 0.7773 (ttm) REVERT: D 316 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7538 (mp0) REVERT: D 334 GLU cc_start: 0.7850 (mp0) cc_final: 0.7378 (tm-30) REVERT: E 57 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7836 (mp0) REVERT: E 96 VAL cc_start: 0.8265 (p) cc_final: 0.7959 (m) REVERT: E 121 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8445 (tm-30) REVERT: E 123 MET cc_start: 0.8074 (tpp) cc_final: 0.7460 (tpt) REVERT: E 244 ASP cc_start: 0.7572 (p0) cc_final: 0.7293 (t0) outliers start: 29 outliers final: 22 residues processed: 262 average time/residue: 0.2226 time to fit residues: 90.0973 Evaluate side-chains 260 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14910 Z= 0.314 Angle : 0.658 9.415 20255 Z= 0.308 Chirality : 0.047 0.230 2260 Planarity : 0.004 0.035 2570 Dihedral : 9.205 123.424 2120 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.08 % Allowed : 20.19 % Favored : 77.73 % 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: 0.66 (0.20), residues: 1775 helix: 0.66 (0.19), residues: 740 sheet: -0.49 (0.27), residues: 345 loop : 1.02 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.006 0.001 HIS A 371 PHE 0.012 0.001 PHE D 124 TYR 0.012 0.001 TYR E 69 ARG 0.004 0.000 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.693 Fit side-chains revert: symmetry clash REVERT: A 101 HIS cc_start: 0.8253 (m-70) cc_final: 0.8019 (m-70) REVERT: A 113 LYS cc_start: 0.8476 (mttm) cc_final: 0.7247 (mptt) REVERT: A 117 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7459 (mp0) REVERT: A 176 MET cc_start: 0.7547 (mmp) cc_final: 0.7178 (mmt) REVERT: A 325 MET cc_start: 0.8508 (mmp) cc_final: 0.8228 (mmt) REVERT: B 51 ASP cc_start: 0.8095 (m-30) cc_final: 0.7864 (t0) REVERT: B 143 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7347 (t80) REVERT: C 57 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7610 (mt-10) REVERT: C 95 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8650 (ttm-80) REVERT: C 143 TYR cc_start: 0.7906 (m-80) cc_final: 0.7590 (m-10) REVERT: C 313 MET cc_start: 0.8246 (tpp) cc_final: 0.8031 (tpp) REVERT: D 88 HIS cc_start: 0.7860 (t70) cc_final: 0.7616 (t70) REVERT: D 140 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8757 (mt) REVERT: D 143 TYR cc_start: 0.7735 (m-80) cc_final: 0.7416 (m-80) REVERT: D 162 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8201 (t0) REVERT: D 176 MET cc_start: 0.7767 (mmp) cc_final: 0.7364 (mmp) REVERT: D 316 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7577 (mp0) REVERT: D 334 GLU cc_start: 0.7904 (mp0) cc_final: 0.7453 (tm-30) REVERT: E 57 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7887 (mp0) REVERT: E 96 VAL cc_start: 0.8379 (p) cc_final: 0.8060 (m) REVERT: E 121 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8386 (tm-30) outliers start: 32 outliers final: 25 residues processed: 249 average time/residue: 0.2325 time to fit residues: 89.4586 Evaluate side-chains 243 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.101419 restraints weight = 21197.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104158 restraints weight = 12355.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106071 restraints weight = 8037.552| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14910 Z= 0.234 Angle : 0.629 13.376 20255 Z= 0.290 Chirality : 0.046 0.225 2260 Planarity : 0.004 0.034 2570 Dihedral : 8.951 127.867 2120 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.88 % Allowed : 20.84 % Favored : 77.27 % 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: 0.64 (0.20), residues: 1775 helix: 0.66 (0.19), residues: 740 sheet: -0.49 (0.27), residues: 345 loop : 0.97 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.006 0.001 HIS D 161 PHE 0.009 0.001 PHE D 352 TYR 0.010 0.001 TYR A 306 ARG 0.004 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2873.88 seconds wall clock time: 52 minutes 52.16 seconds (3172.16 seconds total)