Starting phenix.real_space_refine on Mon Mar 11 08:07:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4c_16424/03_2024/8c4c_16424_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4c_16424/03_2024/8c4c_16424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4c_16424/03_2024/8c4c_16424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4c_16424/03_2024/8c4c_16424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4c_16424/03_2024/8c4c_16424_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4c_16424/03_2024/8c4c_16424_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 184 5.16 5 C 17852 2.51 5 N 4796 2.21 5 O 5436 1.98 5 H 27792 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ASP 311": "OD1" <-> "OD2" Residue "G GLU 364": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 286": "OD1" <-> "OD2" Residue "H ASP 288": "OD1" <-> "OD2" Residue "K ASP 569": "OD1" <-> "OD2" Residue "K ASP 579": "OD1" <-> "OD2" Residue "K ASP 592": "OD1" <-> "OD2" Residue "L GLU 544": "OE1" <-> "OE2" Residue "L ASP 557": "OD1" <-> "OD2" Residue "L PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 569": "OD1" <-> "OD2" Residue "L ASP 579": "OD1" <-> "OD2" Residue "L ASP 594": "OD1" <-> "OD2" Residue "L GLU 629": "OE1" <-> "OE2" Residue "M ASP 557": "OD1" <-> "OD2" Residue "M ASP 569": "OD1" <-> "OD2" Residue "M GLU 574": "OE1" <-> "OE2" Residue "M ASP 579": "OD1" <-> "OD2" Residue "M GLU 617": "OE1" <-> "OE2" Residue "M TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 541": "OD1" <-> "OD2" Residue "N GLU 555": "OE1" <-> "OE2" Residue "N PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 579": "OD1" <-> "OD2" Residue "N GLU 598": "OE1" <-> "OE2" Residue "N GLU 604": "OE1" <-> "OE2" Residue "N GLU 608": "OE1" <-> "OE2" Residue "N GLU 617": "OE1" <-> "OE2" Residue "N GLU 638": "OE1" <-> "OE2" Residue "N TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 56092 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: "G" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: "H" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5751 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: "K" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2455 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "L" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2455 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "M" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2455 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "N" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2455 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.95, per 1000 atoms: 0.32 Number of scatterers: 56092 At special positions: 0 Unit cell: (99.12, 119.77, 271.754, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 184 16.00 P 24 15.00 Mg 8 11.99 O 5436 8.00 N 4796 7.00 C 17852 6.00 H 27792 1.00 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: 35.40 Conformation dependent library (CDL) restraints added in 4.1 seconds 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 202 helices and 35 sheets defined 46.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.53 Creating SS restraints... Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 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 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 185 through 196 removed outlier: 4.214A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 removed outlier: 3.610A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.714A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.757A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.284A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.912A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.521A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.625A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.524A 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 274 through 284 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.674A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.690A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.629A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.684A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.535A 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 284 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.287A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.570A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 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 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.751A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.611A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.689A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.499A 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 290 through 294 Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.836A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 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 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.562A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.564A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.736A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.597A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.628A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.605A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 252 through 261 removed outlier: 3.632A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.763A pdb=" N LYS F 373 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 196 removed outlier: 3.724A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 removed outlier: 3.502A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 252 through 261 removed outlier: 3.655A pdb=" N ARG G 256 " --> pdb=" O GLU G 253 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 284 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 338 through 348 Processing helix chain 'G' and resid 350 through 352 No H-bonds generated for 'chain 'G' and resid 350 through 352' Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 373 removed outlier: 3.694A pdb=" N LYS G 373 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.699A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 removed outlier: 3.536A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 252 through 261 removed outlier: 3.667A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 283 Processing helix chain 'H' and resid 287 through 294 removed outlier: 5.399A pdb=" N LYS H 291 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 338 through 347 Processing helix chain 'H' and resid 351 through 354 removed outlier: 3.866A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 351 through 354' Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.611A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 528 No H-bonds generated for 'chain 'K' and resid 526 through 528' Processing helix chain 'K' and resid 532 through 536 Processing helix chain 'K' and resid 542 through 553 Processing helix chain 'K' and resid 562 through 575 Processing helix chain 'K' and resid 580 through 589 Processing helix chain 'K' and resid 593 through 595 No H-bonds generated for 'chain 'K' and resid 593 through 595' Processing helix chain 'K' and resid 597 through 612 Processing helix chain 'K' and resid 616 through 630 Processing helix chain 'K' and resid 636 through 638 No H-bonds generated for 'chain 'K' and resid 636 through 638' Processing helix chain 'K' and resid 641 through 650 Processing helix chain 'K' and resid 655 through 657 No H-bonds generated for 'chain 'K' and resid 655 through 657' Processing helix chain 'L' and resid 526 through 528 No H-bonds generated for 'chain 'L' and resid 526 through 528' Processing helix chain 'L' and resid 532 through 536 removed outlier: 3.585A pdb=" N HIS L 536 " --> pdb=" O VAL L 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 532 through 536' Processing helix chain 'L' and resid 542 through 553 Processing helix chain 'L' and resid 562 through 575 Processing helix chain 'L' and resid 580 through 595 removed outlier: 4.360A pdb=" N ASP L 592 " --> pdb=" O ALA L 588 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE L 593 " --> pdb=" O GLN L 589 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP L 594 " --> pdb=" O CYS L 590 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS L 595 " --> pdb=" O SER L 591 " (cutoff:3.500A) Processing helix chain 'L' and resid 597 through 611 Processing helix chain 'L' and resid 616 through 630 Processing helix chain 'L' and resid 636 through 638 No H-bonds generated for 'chain 'L' and resid 636 through 638' Processing helix chain 'L' and resid 641 through 650 Processing helix chain 'L' and resid 655 through 657 No H-bonds generated for 'chain 'L' and resid 655 through 657' Processing helix chain 'M' and resid 526 through 528 No H-bonds generated for 'chain 'M' and resid 526 through 528' Processing helix chain 'M' and resid 532 through 536 removed outlier: 3.609A pdb=" N HIS M 536 " --> pdb=" O VAL M 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 532 through 536' Processing helix chain 'M' and resid 542 through 553 Processing helix chain 'M' and resid 562 through 575 Processing helix chain 'M' and resid 580 through 589 Processing helix chain 'M' and resid 593 through 595 No H-bonds generated for 'chain 'M' and resid 593 through 595' Processing helix chain 'M' and resid 597 through 612 Processing helix chain 'M' and resid 616 through 630 Processing helix chain 'M' and resid 636 through 638 No H-bonds generated for 'chain 'M' and resid 636 through 638' Processing helix chain 'M' and resid 641 through 650 Processing helix chain 'M' and resid 655 through 658 Processing helix chain 'N' and resid 526 through 528 No H-bonds generated for 'chain 'N' and resid 526 through 528' Processing helix chain 'N' and resid 532 through 536 removed outlier: 3.552A pdb=" N HIS N 536 " --> pdb=" O VAL N 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 532 through 536' Processing helix chain 'N' and resid 542 through 553 Processing helix chain 'N' and resid 562 through 575 Processing helix chain 'N' and resid 580 through 590 Processing helix chain 'N' and resid 593 through 595 No H-bonds generated for 'chain 'N' and resid 593 through 595' Processing helix chain 'N' and resid 597 through 611 Processing helix chain 'N' and resid 616 through 630 Processing helix chain 'N' and resid 636 through 638 No H-bonds generated for 'chain 'N' and resid 636 through 638' Processing helix chain 'N' and resid 641 through 650 Processing helix chain 'N' and resid 655 through 657 No H-bonds generated for 'chain 'N' and resid 655 through 657' Processing sheet with id= A, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.354A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (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: 6.705A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.200A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.177A 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: 6.697A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.464A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.152A 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: 6.704A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.389A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.257A 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 8 through 12 Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= T, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.329A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= V, first strand: chain 'F' and resid 8 through 12 Processing sheet with id= W, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= X, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= Y, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.309A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= AA, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.612A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 35 through 38 Processing sheet with id= AC, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.394A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 Processing sheet with id= AE, first strand: chain 'H' and resid 8 through 12 removed outlier: 3.518A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 35 through 38 Processing sheet with id= AG, first strand: chain 'H' and resid 103 through 107 Processing sheet with id= AH, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.499A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 238 through 241 1058 hydrogen bonds defined for protein. 2814 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: 21.24 Time building geometry restraints manager: 37.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 27748 1.03 - 1.23: 47 1.23 - 1.42: 11861 1.42 - 1.62: 16724 1.62 - 1.81: 324 Bond restraints: 56704 Sorted by residual: bond pdb=" O3 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.12e+00 bond pdb=" O3 PO4 G 401 " pdb=" P PO4 G 401 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" O3 PO4 E 803 " pdb=" P PO4 E 803 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" O3 PO4 B 401 " pdb=" P PO4 B 401 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" O3 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.02e+00 ... (remaining 56699 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.70: 764 105.70 - 113.34: 67354 113.34 - 120.99: 22313 120.99 - 128.64: 11898 128.64 - 136.29: 215 Bond angle restraints: 102544 Sorted by residual: angle pdb=" C LYS M 636 " pdb=" CA LYS M 636 " pdb=" CB LYS M 636 " ideal model delta sigma weight residual 117.23 111.04 6.19 1.36e+00 5.41e-01 2.07e+01 angle pdb=" C LYS N 636 " pdb=" CA LYS N 636 " pdb=" CB LYS N 636 " ideal model delta sigma weight residual 117.23 111.20 6.03 1.36e+00 5.41e-01 1.97e+01 angle pdb=" C GLY B 42 " pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 121.70 129.23 -7.53 1.80e+00 3.09e-01 1.75e+01 angle pdb=" C GLY C 42 " pdb=" N VAL C 43 " pdb=" CA VAL C 43 " ideal model delta sigma weight residual 121.70 129.21 -7.51 1.80e+00 3.09e-01 1.74e+01 angle pdb=" C GLY F 42 " pdb=" N VAL F 43 " pdb=" CA VAL F 43 " ideal model delta sigma weight residual 121.70 128.91 -7.21 1.80e+00 3.09e-01 1.60e+01 ... (remaining 102539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.08: 24535 21.08 - 42.17: 1584 42.17 - 63.25: 532 63.25 - 84.33: 60 84.33 - 105.42: 21 Dihedral angle restraints: 26732 sinusoidal: 14704 harmonic: 12028 Sorted by residual: dihedral pdb=" CA VAL A 9 " pdb=" C VAL A 9 " pdb=" N CYS A 10 " pdb=" CA CYS A 10 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" C5' ADP E 802 " pdb=" O5' ADP E 802 " pdb=" PA ADP E 802 " pdb=" O2A ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 45.42 -105.42 1 2.00e+01 2.50e-03 3.04e+01 dihedral pdb=" CA CYS A 10 " pdb=" C CYS A 10 " pdb=" N ASP A 11 " pdb=" CA ASP A 11 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 26729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2718 0.030 - 0.061: 1109 0.061 - 0.091: 228 0.091 - 0.121: 269 0.121 - 0.151: 20 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE E 357 " pdb=" N ILE E 357 " pdb=" C ILE E 357 " pdb=" CB ILE E 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE H 357 " pdb=" N ILE H 357 " pdb=" C ILE H 357 " pdb=" CB ILE H 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 4341 not shown) Planarity restraints: 8392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 592 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" CG ASP K 592 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP K 592 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP K 592 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 95 " 0.151 9.50e-02 1.11e+02 5.07e-02 3.19e+00 pdb=" NE ARG D 95 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 95 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 95 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 95 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 95 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG D 95 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 95 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 95 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 566 " 0.148 9.50e-02 1.11e+02 4.97e-02 3.10e+00 pdb=" NE ARG L 566 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG L 566 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG L 566 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG L 566 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG L 566 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG L 566 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG L 566 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG L 566 " -0.001 2.00e-02 2.50e+03 ... (remaining 8389 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 1236 2.08 - 2.71: 94560 2.71 - 3.34: 172942 3.34 - 3.97: 227607 3.97 - 4.60: 352832 Nonbonded interactions: 849177 Sorted by model distance: nonbonded pdb=" OE1 GLN H 49 " pdb=" H GLN H 49 " model vdw 1.456 1.850 nonbonded pdb=" O GLY A 168 " pdb=" H VAL C 43 " model vdw 1.541 1.850 nonbonded pdb=" OE1 GLU M 598 " pdb=" H GLU M 598 " model vdw 1.550 1.850 nonbonded pdb=" O TYR B 362 " pdb=" H GLY B 366 " model vdw 1.555 1.850 nonbonded pdb=" HZ2 LYS C 213 " pdb=" O2' ADP C 401 " model vdw 1.568 1.850 ... (remaining 849172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 375) selection = (chain 'B' and resid 6 through 375) selection = (chain 'C' and resid 6 through 375) selection = (chain 'D' and resid 6 through 375) selection = (chain 'E' and resid 6 through 375) selection = (chain 'F' and resid 6 through 375) selection = (chain 'G' and resid 6 through 375) selection = (chain 'H' and resid 6 through 375) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.610 Extract box with map and model: 23.960 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 139.340 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28912 Z= 0.221 Angle : 0.585 7.535 39208 Z= 0.296 Chirality : 0.041 0.151 4344 Planarity : 0.003 0.066 5016 Dihedral : 15.853 105.415 10780 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Rotamer: Outliers : 0.89 % Allowed : 11.69 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.30 (0.15), residues: 3536 helix: 0.92 (0.14), residues: 1580 sheet: -0.31 (0.26), residues: 360 loop : 1.38 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.006 0.001 HIS A 40 PHE 0.010 0.001 PHE A 255 TYR 0.009 0.001 TYR C 143 ARG 0.010 0.000 ARG L 566 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 497 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.1178 (tpt) cc_final: 0.0666 (tpt) REVERT: A 81 ASP cc_start: 0.7955 (m-30) cc_final: 0.7596 (m-30) REVERT: A 157 ASP cc_start: 0.7867 (t70) cc_final: 0.7054 (t0) REVERT: A 190 MET cc_start: 0.8114 (ptp) cc_final: 0.7823 (ptp) REVERT: A 191 LYS cc_start: 0.7683 (tttp) cc_final: 0.7371 (tttp) REVERT: A 205 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 224 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6595 (mp0) REVERT: A 227 MET cc_start: 0.8050 (mmt) cc_final: 0.7474 (mmm) REVERT: A 291 LYS cc_start: 0.8235 (ttpp) cc_final: 0.7864 (ttmm) REVERT: A 334 GLU cc_start: 0.6736 (pm20) cc_final: 0.6129 (pp20) REVERT: A 357 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7838 (mt) REVERT: B 95 ARG cc_start: 0.6926 (mtt-85) cc_final: 0.6710 (mtt-85) REVERT: B 187 ASP cc_start: 0.8132 (m-30) cc_final: 0.7732 (m-30) REVERT: B 191 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7362 (tttm) REVERT: B 241 GLU cc_start: 0.7884 (tt0) cc_final: 0.7633 (tt0) REVERT: B 283 MET cc_start: 0.8577 (mmm) cc_final: 0.8285 (mmm) REVERT: B 297 ASN cc_start: 0.8959 (m110) cc_final: 0.8747 (m110) REVERT: B 328 LYS cc_start: 0.8033 (tttp) cc_final: 0.7710 (ttpp) REVERT: B 372 ARG cc_start: 0.6986 (mtm-85) cc_final: 0.6658 (mtm180) REVERT: C 24 ASP cc_start: 0.7898 (m-30) cc_final: 0.7660 (m-30) REVERT: C 25 ASP cc_start: 0.7508 (p0) cc_final: 0.7119 (p0) REVERT: C 68 LYS cc_start: 0.7919 (mttm) cc_final: 0.7718 (mtmt) REVERT: C 72 GLU cc_start: 0.7351 (tt0) cc_final: 0.7130 (mt-10) REVERT: C 83 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7564 (tt0) REVERT: C 190 MET cc_start: 0.7976 (ptm) cc_final: 0.7724 (mtp) REVERT: C 276 GLU cc_start: 0.7723 (tt0) cc_final: 0.7266 (mt-10) REVERT: C 284 LYS cc_start: 0.8079 (mttt) cc_final: 0.7736 (mttm) REVERT: C 334 GLU cc_start: 0.7053 (pm20) cc_final: 0.6703 (pm20) REVERT: C 359 LYS cc_start: 0.7689 (tptm) cc_final: 0.7379 (tptt) REVERT: C 360 GLN cc_start: 0.6620 (tm-30) cc_final: 0.6402 (tt0) REVERT: C 363 ASP cc_start: 0.7033 (m-30) cc_final: 0.6806 (m-30) REVERT: D 72 GLU cc_start: 0.7423 (pt0) cc_final: 0.7137 (mt-10) REVERT: D 95 ARG cc_start: 0.7289 (mtt-85) cc_final: 0.6766 (mmt90) REVERT: D 206 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7525 (ttm110) REVERT: D 225 ASN cc_start: 0.6984 (m-40) cc_final: 0.6728 (t0) REVERT: D 276 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7464 (mt-10) REVERT: D 298 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7736 (t) REVERT: E 95 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6578 (mmt90) REVERT: E 128 ASN cc_start: 0.7339 (m110) cc_final: 0.6501 (t0) REVERT: E 178 LEU cc_start: 0.7574 (tp) cc_final: 0.7312 (tp) REVERT: E 191 LYS cc_start: 0.8039 (tttm) cc_final: 0.7198 (tttt) REVERT: E 299 MET cc_start: 0.8798 (mmm) cc_final: 0.8560 (mtp) REVERT: E 328 LYS cc_start: 0.7908 (tttt) cc_final: 0.7114 (mttp) REVERT: E 334 GLU cc_start: 0.7319 (pm20) cc_final: 0.7021 (pm20) REVERT: E 360 GLN cc_start: 0.7336 (tt0) cc_final: 0.6430 (pm20) REVERT: F 49 GLN cc_start: 0.6839 (mt0) cc_final: 0.6581 (mm110) REVERT: F 51 ASP cc_start: 0.7302 (p0) cc_final: 0.7073 (p0) REVERT: F 61 LYS cc_start: 0.7822 (mttm) cc_final: 0.7616 (mtmm) REVERT: F 72 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7169 (mm-30) REVERT: F 80 ASP cc_start: 0.7847 (m-30) cc_final: 0.7400 (m-30) REVERT: F 95 ARG cc_start: 0.7067 (mtp85) cc_final: 0.6654 (mtt-85) REVERT: F 125 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7242 (mm-30) REVERT: F 162 ASN cc_start: 0.8354 (m110) cc_final: 0.8009 (m110) REVERT: F 167 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8209 (mm-30) REVERT: F 206 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7257 (ttm110) REVERT: F 226 GLU cc_start: 0.7864 (tp30) cc_final: 0.7581 (tp30) REVERT: F 326 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.6652 (ptmm) REVERT: F 328 LYS cc_start: 0.8205 (tttp) cc_final: 0.7747 (tptm) REVERT: F 334 GLU cc_start: 0.7042 (pm20) cc_final: 0.6700 (pm20) REVERT: F 354 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7440 (mm110) REVERT: F 358 THR cc_start: 0.7786 (m) cc_final: 0.7103 (p) REVERT: G 25 ASP cc_start: 0.7131 (p0) cc_final: 0.6814 (m-30) REVERT: G 95 ARG cc_start: 0.7295 (mtt-85) cc_final: 0.6933 (mtm110) REVERT: G 118 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7340 (mmmm) REVERT: G 190 MET cc_start: 0.8611 (mtp) cc_final: 0.8341 (ttm) REVERT: G 224 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7192 (mm-30) REVERT: G 227 MET cc_start: 0.7977 (mmm) cc_final: 0.7704 (mmm) REVERT: G 246 GLN cc_start: 0.7923 (mt0) cc_final: 0.7386 (mt0) REVERT: G 292 ASP cc_start: 0.8053 (m-30) cc_final: 0.7780 (m-30) REVERT: G 326 LYS cc_start: 0.7596 (mmtm) cc_final: 0.6929 (mmtp) REVERT: G 355 MET cc_start: 0.8307 (mmm) cc_final: 0.7806 (mtt) REVERT: H 24 ASP cc_start: 0.6798 (m-30) cc_final: 0.6458 (m-30) REVERT: H 25 ASP cc_start: 0.6633 (p0) cc_final: 0.6329 (p0) REVERT: H 68 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7982 (mptt) REVERT: H 72 GLU cc_start: 0.7408 (tt0) cc_final: 0.7034 (mt-10) REVERT: H 93 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7164 (mm-30) REVERT: H 113 LYS cc_start: 0.5103 (mptt) cc_final: 0.4154 (mmtm) REVERT: H 117 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7133 (mt-10) REVERT: H 167 GLU cc_start: 0.7653 (mp0) cc_final: 0.7439 (mm-30) REVERT: H 206 ARG cc_start: 0.7789 (ttm110) cc_final: 0.7355 (ttp-110) REVERT: H 226 GLU cc_start: 0.7911 (tp30) cc_final: 0.7670 (tp30) REVERT: H 286 ASP cc_start: 0.6402 (m-30) cc_final: 0.6010 (m-30) REVERT: H 292 ASP cc_start: 0.7820 (m-30) cc_final: 0.7574 (m-30) REVERT: H 299 MET cc_start: 0.8344 (mtp) cc_final: 0.8129 (mmm) REVERT: H 305 MET cc_start: 0.8212 (mmm) cc_final: 0.7974 (tpp) REVERT: H 314 GLN cc_start: 0.7624 (tp40) cc_final: 0.7190 (tp40) REVERT: H 326 LYS cc_start: 0.7009 (mmpt) cc_final: 0.6707 (pttm) REVERT: H 328 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7080 (tmtt) REVERT: H 336 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7768 (tttt) REVERT: H 355 MET cc_start: 0.7649 (mpt) cc_final: 0.7436 (mpt) REVERT: H 360 GLN cc_start: 0.6652 (tm130) cc_final: 0.5990 (tp-100) REVERT: K 538 MET cc_start: 0.7860 (ttm) cc_final: 0.7454 (ttm) REVERT: K 578 ASN cc_start: 0.6340 (t0) cc_final: 0.6017 (t0) REVERT: K 595 LYS cc_start: 0.5970 (mmtp) cc_final: 0.5673 (mmtp) REVERT: K 598 GLU cc_start: 0.5788 (pm20) cc_final: 0.5172 (pt0) REVERT: K 603 MET cc_start: 0.7304 (tpt) cc_final: 0.7078 (tpt) REVERT: K 617 GLU cc_start: 0.6685 (mp0) cc_final: 0.6466 (mt-10) REVERT: K 621 GLU cc_start: 0.7340 (tt0) cc_final: 0.6851 (mt-10) REVERT: K 629 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6941 (mm-30) REVERT: K 664 SER cc_start: 0.6627 (t) cc_final: 0.6201 (p) REVERT: L 574 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6962 (tm-30) REVERT: L 578 ASN cc_start: 0.7245 (p0) cc_final: 0.7044 (p0) REVERT: L 582 LYS cc_start: 0.6423 (mtpt) cc_final: 0.5931 (mmtp) REVERT: L 604 GLU cc_start: 0.6593 (mm-30) cc_final: 0.5893 (tp30) REVERT: L 608 GLU cc_start: 0.6889 (tp30) cc_final: 0.6679 (mm-30) REVERT: L 629 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7121 (mp0) REVERT: M 527 SER cc_start: 0.8179 (m) cc_final: 0.7819 (p) REVERT: M 533 THR cc_start: 0.8034 (m) cc_final: 0.7657 (p) REVERT: M 541 ASP cc_start: 0.7512 (t0) cc_final: 0.6764 (t0) REVERT: M 557 ASP cc_start: 0.7118 (t0) cc_final: 0.6590 (t70) REVERT: M 604 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6167 (tt0) REVERT: M 634 ARG cc_start: 0.6812 (ttp80) cc_final: 0.6436 (ttp-110) REVERT: M 644 SER cc_start: 0.7029 (p) cc_final: 0.6789 (m) REVERT: M 664 SER cc_start: 0.5236 (t) cc_final: 0.4871 (t) REVERT: M 665 TYR cc_start: 0.6146 (m-80) cc_final: 0.5758 (m-80) REVERT: N 521 LYS cc_start: 0.7030 (ttpp) cc_final: 0.6694 (tttp) REVERT: N 544 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6582 (tp30) REVERT: N 557 ASP cc_start: 0.6732 (t0) cc_final: 0.6476 (t70) REVERT: N 574 GLU cc_start: 0.6888 (tt0) cc_final: 0.6605 (tt0) REVERT: N 603 MET cc_start: 0.6173 (tpt) cc_final: 0.5584 (tpt) REVERT: N 621 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6421 (mt-10) REVERT: N 663 GLU cc_start: 0.5069 (tp30) cc_final: 0.4710 (tp30) outliers start: 27 outliers final: 22 residues processed: 519 average time/residue: 2.8340 time to fit residues: 1695.6801 Evaluate side-chains 389 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 364 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 297 ASN D 297 ASN G 49 GLN G 225 ASN G 360 GLN H 128 ASN K 645 ASN M 589 GLN M 625 GLN N 589 GLN N 645 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28912 Z= 0.326 Angle : 0.649 7.495 39208 Z= 0.329 Chirality : 0.045 0.172 4344 Planarity : 0.005 0.041 5016 Dihedral : 8.257 124.299 4036 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 2.61 % Allowed : 12.42 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.92 (0.14), residues: 3536 helix: 0.60 (0.13), residues: 1596 sheet: -0.53 (0.22), residues: 480 loop : 1.37 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.021 0.002 PHE K 568 TYR 0.012 0.002 TYR L 665 ARG 0.006 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 346 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8132 (m-30) cc_final: 0.7729 (m-30) REVERT: A 100 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7206 (pt0) REVERT: A 190 MET cc_start: 0.7805 (ptp) cc_final: 0.7525 (ptm) REVERT: A 191 LYS cc_start: 0.7487 (tttp) cc_final: 0.7188 (tttp) REVERT: A 205 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6991 (mt-10) REVERT: A 224 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6766 (tp30) REVERT: A 227 MET cc_start: 0.8081 (mmt) cc_final: 0.7546 (mmm) REVERT: A 288 ASP cc_start: 0.8024 (m-30) cc_final: 0.7812 (m-30) REVERT: A 291 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7501 (ttmm) REVERT: A 334 GLU cc_start: 0.6753 (pm20) cc_final: 0.6233 (pp20) REVERT: A 357 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7840 (mt) REVERT: B 47 MET cc_start: 0.1581 (OUTLIER) cc_final: 0.0402 (ptm) REVERT: B 95 ARG cc_start: 0.6943 (mtt-85) cc_final: 0.6658 (mtt-85) REVERT: B 328 LYS cc_start: 0.8063 (tttp) cc_final: 0.7748 (ttpp) REVERT: B 372 ARG cc_start: 0.7033 (mtm-85) cc_final: 0.6694 (mtm180) REVERT: C 24 ASP cc_start: 0.7835 (m-30) cc_final: 0.7607 (m-30) REVERT: C 25 ASP cc_start: 0.7540 (p0) cc_final: 0.7171 (p0) REVERT: C 68 LYS cc_start: 0.8003 (mttm) cc_final: 0.7607 (mtmt) REVERT: C 72 GLU cc_start: 0.7408 (tt0) cc_final: 0.7202 (mt-10) REVERT: C 83 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: C 99 GLU cc_start: 0.7492 (pm20) cc_final: 0.7176 (pm20) REVERT: C 107 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: C 276 GLU cc_start: 0.7830 (tt0) cc_final: 0.7329 (mt-10) REVERT: C 328 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7268 (ttmm) REVERT: C 334 GLU cc_start: 0.7341 (pm20) cc_final: 0.7006 (pm20) REVERT: C 355 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7402 (mmt) REVERT: C 359 LYS cc_start: 0.7636 (tptm) cc_final: 0.7315 (tptt) REVERT: C 363 ASP cc_start: 0.7065 (m-30) cc_final: 0.6818 (m-30) REVERT: D 72 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: D 84 LYS cc_start: 0.8102 (ptpp) cc_final: 0.7872 (ptpp) REVERT: D 95 ARG cc_start: 0.7451 (mtt-85) cc_final: 0.6913 (mmt90) REVERT: D 276 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7617 (tt0) REVERT: D 298 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7892 (t) REVERT: E 95 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6572 (mmt90) REVERT: E 128 ASN cc_start: 0.7470 (m110) cc_final: 0.6573 (t0) REVERT: E 178 LEU cc_start: 0.7907 (tp) cc_final: 0.7688 (tp) REVERT: E 328 LYS cc_start: 0.7895 (tttt) cc_final: 0.7086 (mttp) REVERT: E 334 GLU cc_start: 0.7540 (pm20) cc_final: 0.7165 (pm20) REVERT: E 351 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7119 (m) REVERT: E 360 GLN cc_start: 0.7204 (tt0) cc_final: 0.6581 (pm20) REVERT: F 49 GLN cc_start: 0.6791 (mt0) cc_final: 0.6511 (mm110) REVERT: F 51 ASP cc_start: 0.7338 (p0) cc_final: 0.7108 (p0) REVERT: F 72 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7251 (mm-30) REVERT: F 80 ASP cc_start: 0.7697 (m-30) cc_final: 0.7309 (m-30) REVERT: F 95 ARG cc_start: 0.7073 (mtp85) cc_final: 0.6639 (mtt-85) REVERT: F 125 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7266 (mm-30) REVERT: F 162 ASN cc_start: 0.8280 (m110) cc_final: 0.8057 (m110) REVERT: F 167 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8231 (mm-30) REVERT: F 206 ARG cc_start: 0.7625 (ttm110) cc_final: 0.7215 (ttm110) REVERT: F 226 GLU cc_start: 0.7905 (tp30) cc_final: 0.7538 (tp30) REVERT: F 326 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.6649 (ptmm) REVERT: F 328 LYS cc_start: 0.8172 (tttp) cc_final: 0.7732 (tptm) REVERT: F 334 GLU cc_start: 0.7373 (pm20) cc_final: 0.7149 (pm20) REVERT: F 354 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7398 (mm110) REVERT: F 360 GLN cc_start: 0.7119 (tt0) cc_final: 0.6811 (tt0) REVERT: F 363 ASP cc_start: 0.7406 (m-30) cc_final: 0.7075 (m-30) REVERT: G 95 ARG cc_start: 0.7369 (mtt-85) cc_final: 0.6935 (mtm180) REVERT: G 113 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7702 (mmtp) REVERT: G 118 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7191 (mmmm) REVERT: G 123 MET cc_start: 0.8498 (mmp) cc_final: 0.8161 (mmp) REVERT: G 292 ASP cc_start: 0.7992 (m-30) cc_final: 0.7761 (m-30) REVERT: G 326 LYS cc_start: 0.7682 (mmtm) cc_final: 0.7035 (mmtp) REVERT: G 355 MET cc_start: 0.8014 (mmm) cc_final: 0.7808 (mtt) REVERT: H 24 ASP cc_start: 0.6791 (m-30) cc_final: 0.6437 (m-30) REVERT: H 25 ASP cc_start: 0.6802 (p0) cc_final: 0.6358 (p0) REVERT: H 68 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7933 (mptt) REVERT: H 72 GLU cc_start: 0.7708 (tt0) cc_final: 0.7252 (mt-10) REVERT: H 93 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7201 (mm-30) REVERT: H 113 LYS cc_start: 0.5114 (OUTLIER) cc_final: 0.4693 (mppt) REVERT: H 167 GLU cc_start: 0.7756 (mp0) cc_final: 0.7532 (mm-30) REVERT: H 176 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7717 (mtp) REVERT: H 206 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7350 (ttp-110) REVERT: H 276 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7371 (mt-10) REVERT: H 286 ASP cc_start: 0.6412 (m-30) cc_final: 0.6037 (m-30) REVERT: H 299 MET cc_start: 0.8349 (mtp) cc_final: 0.8134 (mmm) REVERT: H 314 GLN cc_start: 0.7634 (tp40) cc_final: 0.7276 (tp40) REVERT: H 326 LYS cc_start: 0.7031 (mmpt) cc_final: 0.6760 (pttm) REVERT: H 328 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7087 (tmtt) REVERT: H 336 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7758 (ttpt) REVERT: H 354 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6922 (tp40) REVERT: K 538 MET cc_start: 0.7949 (ttm) cc_final: 0.7567 (ttm) REVERT: K 541 ASP cc_start: 0.7182 (t0) cc_final: 0.6671 (t70) REVERT: K 578 ASN cc_start: 0.6493 (t0) cc_final: 0.6175 (t0) REVERT: K 595 LYS cc_start: 0.5805 (mmtp) cc_final: 0.5563 (mmtp) REVERT: K 598 GLU cc_start: 0.5946 (pm20) cc_final: 0.5277 (pt0) REVERT: K 603 MET cc_start: 0.7364 (tpt) cc_final: 0.7113 (tpt) REVERT: K 608 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6171 (mm-30) REVERT: K 617 GLU cc_start: 0.6506 (mp0) cc_final: 0.6250 (mt-10) REVERT: K 621 GLU cc_start: 0.7364 (tt0) cc_final: 0.7015 (mt-10) REVERT: K 664 SER cc_start: 0.6732 (t) cc_final: 0.6235 (p) REVERT: L 574 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6566 (tp30) REVERT: L 582 LYS cc_start: 0.6410 (mtpt) cc_final: 0.5958 (mmtp) REVERT: L 608 GLU cc_start: 0.6987 (tp30) cc_final: 0.6746 (mm-30) REVERT: M 521 LYS cc_start: 0.6679 (tttp) cc_final: 0.6121 (tttm) REVERT: M 533 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7635 (p) REVERT: M 541 ASP cc_start: 0.7486 (t0) cc_final: 0.6826 (t0) REVERT: M 604 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6102 (tt0) REVERT: M 625 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6577 (tt0) REVERT: M 634 ARG cc_start: 0.6811 (ttp80) cc_final: 0.6513 (ttp-110) REVERT: M 644 SER cc_start: 0.7109 (p) cc_final: 0.6900 (m) REVERT: M 664 SER cc_start: 0.5122 (t) cc_final: 0.4843 (t) REVERT: M 665 TYR cc_start: 0.6195 (m-80) cc_final: 0.5936 (m-80) REVERT: N 521 LYS cc_start: 0.7163 (ttpp) cc_final: 0.6959 (ttmm) REVERT: N 528 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7848 (p) REVERT: N 557 ASP cc_start: 0.6941 (t0) cc_final: 0.6715 (t70) REVERT: N 566 ARG cc_start: 0.6463 (ttt180) cc_final: 0.6245 (mtt180) REVERT: N 663 GLU cc_start: 0.5041 (tp30) cc_final: 0.4736 (tp30) outliers start: 79 outliers final: 34 residues processed: 401 average time/residue: 2.7410 time to fit residues: 1290.1833 Evaluate side-chains 375 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 324 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 625 GLN Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 269 optimal weight: 0.1980 chunk 220 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 323 optimal weight: 4.9990 chunk 349 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 321 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN F 297 ASN G 49 GLN G 225 ASN N 589 GLN N 645 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28912 Z= 0.184 Angle : 0.572 7.316 39208 Z= 0.282 Chirality : 0.042 0.167 4344 Planarity : 0.004 0.039 5016 Dihedral : 7.809 116.712 4025 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 13.01 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.99 (0.14), residues: 3536 helix: 0.72 (0.13), residues: 1596 sheet: -0.41 (0.25), residues: 368 loop : 1.14 (0.17), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.014 0.001 PHE K 568 TYR 0.007 0.001 TYR G 91 ARG 0.005 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 338 time to evaluate : 3.806 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8109 (m-30) cc_final: 0.7710 (m-30) REVERT: A 190 MET cc_start: 0.7811 (ptp) cc_final: 0.7533 (ptm) REVERT: A 191 LYS cc_start: 0.7414 (tttp) cc_final: 0.7138 (tttp) REVERT: A 205 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 224 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6721 (tp30) REVERT: A 227 MET cc_start: 0.8030 (mmt) cc_final: 0.7520 (mmm) REVERT: A 284 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7532 (mttm) REVERT: A 288 ASP cc_start: 0.7989 (m-30) cc_final: 0.7787 (m-30) REVERT: A 291 LYS cc_start: 0.7827 (ttpp) cc_final: 0.7496 (ttmm) REVERT: A 299 MET cc_start: 0.8248 (mmt) cc_final: 0.7797 (mtp) REVERT: A 334 GLU cc_start: 0.6793 (pm20) cc_final: 0.6237 (pp20) REVERT: A 357 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7825 (mt) REVERT: A 360 GLN cc_start: 0.7076 (tt0) cc_final: 0.6643 (tt0) REVERT: B 47 MET cc_start: 0.1411 (OUTLIER) cc_final: 0.0954 (mmm) REVERT: B 328 LYS cc_start: 0.8029 (tttp) cc_final: 0.7518 (mttp) REVERT: B 372 ARG cc_start: 0.7038 (mtm-85) cc_final: 0.6705 (mtm180) REVERT: C 24 ASP cc_start: 0.7838 (m-30) cc_final: 0.7595 (m-30) REVERT: C 25 ASP cc_start: 0.7532 (p0) cc_final: 0.7119 (p0) REVERT: C 68 LYS cc_start: 0.7998 (mttm) cc_final: 0.7612 (mtmt) REVERT: C 83 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7510 (tt0) REVERT: C 99 GLU cc_start: 0.7472 (pm20) cc_final: 0.7143 (pm20) REVERT: C 105 LEU cc_start: 0.8004 (pp) cc_final: 0.7607 (mp) REVERT: C 107 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: C 276 GLU cc_start: 0.7847 (tt0) cc_final: 0.7335 (mt-10) REVERT: C 328 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7247 (ttmm) REVERT: C 334 GLU cc_start: 0.7318 (pm20) cc_final: 0.6993 (pm20) REVERT: C 355 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7476 (mmt) REVERT: C 359 LYS cc_start: 0.7663 (tptm) cc_final: 0.7290 (tptt) REVERT: C 363 ASP cc_start: 0.6948 (m-30) cc_final: 0.6693 (m-30) REVERT: D 72 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: D 95 ARG cc_start: 0.7365 (mtt-85) cc_final: 0.6889 (mmt90) REVERT: D 276 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7601 (mt-10) REVERT: D 298 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7867 (t) REVERT: E 95 ARG cc_start: 0.7093 (mtm-85) cc_final: 0.6553 (mmt90) REVERT: E 128 ASN cc_start: 0.7416 (m110) cc_final: 0.6577 (t0) REVERT: E 178 LEU cc_start: 0.7885 (tp) cc_final: 0.7683 (tp) REVERT: E 225 ASN cc_start: 0.7827 (m-40) cc_final: 0.7624 (m-40) REVERT: E 328 LYS cc_start: 0.7931 (tttt) cc_final: 0.7103 (mttp) REVERT: E 334 GLU cc_start: 0.7576 (pm20) cc_final: 0.7212 (pm20) REVERT: E 360 GLN cc_start: 0.7259 (tt0) cc_final: 0.6642 (pm20) REVERT: F 51 ASP cc_start: 0.7211 (p0) cc_final: 0.7008 (p0) REVERT: F 72 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7233 (mm-30) REVERT: F 80 ASP cc_start: 0.7728 (m-30) cc_final: 0.7344 (m-30) REVERT: F 95 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6632 (mtt-85) REVERT: F 167 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8248 (mm-30) REVERT: F 191 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7751 (tmtt) REVERT: F 206 ARG cc_start: 0.7612 (ttm110) cc_final: 0.7207 (ttm110) REVERT: F 226 GLU cc_start: 0.7915 (tp30) cc_final: 0.7502 (tp30) REVERT: F 326 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.6598 (ptmm) REVERT: F 328 LYS cc_start: 0.8134 (tttp) cc_final: 0.7705 (tptm) REVERT: F 354 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7381 (mm110) REVERT: F 360 GLN cc_start: 0.7153 (tt0) cc_final: 0.6911 (tm-30) REVERT: F 363 ASP cc_start: 0.7411 (m-30) cc_final: 0.7076 (m-30) REVERT: G 95 ARG cc_start: 0.7365 (mtt-85) cc_final: 0.7012 (mtm110) REVERT: G 113 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7670 (mmtp) REVERT: G 118 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7259 (mmmm) REVERT: G 123 MET cc_start: 0.8494 (mmp) cc_final: 0.8207 (mmp) REVERT: G 292 ASP cc_start: 0.7970 (m-30) cc_final: 0.7732 (m-30) REVERT: G 326 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7015 (mmtp) REVERT: G 355 MET cc_start: 0.8039 (mmm) cc_final: 0.7825 (mtt) REVERT: H 24 ASP cc_start: 0.6749 (m-30) cc_final: 0.6391 (m-30) REVERT: H 25 ASP cc_start: 0.6800 (p0) cc_final: 0.6333 (p0) REVERT: H 68 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7950 (mptt) REVERT: H 72 GLU cc_start: 0.7705 (tt0) cc_final: 0.7197 (mt-10) REVERT: H 93 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7097 (mm-30) REVERT: H 113 LYS cc_start: 0.5069 (OUTLIER) cc_final: 0.4666 (mppt) REVERT: H 167 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: H 176 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7771 (mtp) REVERT: H 206 ARG cc_start: 0.7713 (ttm110) cc_final: 0.7333 (ttp-110) REVERT: H 276 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7450 (mt-10) REVERT: H 286 ASP cc_start: 0.6458 (m-30) cc_final: 0.6074 (m-30) REVERT: H 314 GLN cc_start: 0.7644 (tp40) cc_final: 0.7324 (tp40) REVERT: H 326 LYS cc_start: 0.6965 (mmpt) cc_final: 0.6711 (pttm) REVERT: H 328 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7117 (tmtt) REVERT: H 336 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7754 (ttpt) REVERT: H 354 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6833 (tp40) REVERT: K 538 MET cc_start: 0.7920 (ttm) cc_final: 0.7576 (ttm) REVERT: K 541 ASP cc_start: 0.7172 (t0) cc_final: 0.6644 (t70) REVERT: K 578 ASN cc_start: 0.6510 (t0) cc_final: 0.6188 (t0) REVERT: K 595 LYS cc_start: 0.5822 (mmtp) cc_final: 0.5550 (mmtp) REVERT: K 598 GLU cc_start: 0.5979 (pm20) cc_final: 0.5304 (pt0) REVERT: K 603 MET cc_start: 0.7280 (tpt) cc_final: 0.7054 (tpt) REVERT: K 608 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6173 (mm-30) REVERT: K 617 GLU cc_start: 0.6561 (mp0) cc_final: 0.6240 (mt-10) REVERT: K 621 GLU cc_start: 0.7295 (tt0) cc_final: 0.6881 (mt-10) REVERT: K 664 SER cc_start: 0.6682 (t) cc_final: 0.6154 (p) REVERT: L 538 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7754 (mtp) REVERT: L 555 GLU cc_start: 0.7437 (tt0) cc_final: 0.7216 (tt0) REVERT: L 574 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6625 (tp30) REVERT: L 582 LYS cc_start: 0.6327 (mtpt) cc_final: 0.5917 (mmtp) REVERT: L 608 GLU cc_start: 0.6986 (tp30) cc_final: 0.6345 (tt0) REVERT: M 521 LYS cc_start: 0.6655 (tttp) cc_final: 0.6111 (tttm) REVERT: M 527 SER cc_start: 0.8194 (m) cc_final: 0.7837 (p) REVERT: M 533 THR cc_start: 0.7989 (m) cc_final: 0.7622 (p) REVERT: M 541 ASP cc_start: 0.7479 (t0) cc_final: 0.6803 (t0) REVERT: M 557 ASP cc_start: 0.6947 (t0) cc_final: 0.6483 (t70) REVERT: M 604 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6002 (tt0) REVERT: M 664 SER cc_start: 0.5153 (t) cc_final: 0.4880 (t) REVERT: M 665 TYR cc_start: 0.6190 (m-80) cc_final: 0.5919 (m-80) REVERT: N 521 LYS cc_start: 0.7142 (ttpp) cc_final: 0.6937 (ttmm) REVERT: N 528 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7872 (p) REVERT: N 543 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7102 (ttt90) REVERT: N 544 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6412 (tp30) REVERT: N 566 ARG cc_start: 0.6398 (ttt180) cc_final: 0.6180 (mtt180) REVERT: N 663 GLU cc_start: 0.5107 (tp30) cc_final: 0.4839 (tp30) outliers start: 65 outliers final: 32 residues processed: 379 average time/residue: 2.7538 time to fit residues: 1210.5612 Evaluate side-chains 371 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 322 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 538 MET Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 580 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 325 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN D 246 GLN G 49 GLN G 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28912 Z= 0.317 Angle : 0.641 8.007 39208 Z= 0.321 Chirality : 0.045 0.179 4344 Planarity : 0.005 0.054 5016 Dihedral : 8.302 124.857 4024 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 2.91 % Allowed : 12.42 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3536 helix: 0.43 (0.13), residues: 1604 sheet: -0.59 (0.24), residues: 368 loop : 0.97 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 340 HIS 0.007 0.002 HIS A 40 PHE 0.022 0.002 PHE B 266 TYR 0.013 0.002 TYR C 337 ARG 0.005 0.001 ARG L 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 339 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7703 (ptpp) cc_final: 0.7055 (mttp) REVERT: A 81 ASP cc_start: 0.8149 (m-30) cc_final: 0.7758 (m-30) REVERT: A 100 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: A 190 MET cc_start: 0.7802 (ptp) cc_final: 0.7522 (ptm) REVERT: A 191 LYS cc_start: 0.7513 (tttp) cc_final: 0.7202 (ttpp) REVERT: A 205 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6977 (mt-10) REVERT: A 224 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6589 (tp30) REVERT: A 227 MET cc_start: 0.8055 (mmt) cc_final: 0.7517 (mmm) REVERT: A 284 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7606 (mttm) REVERT: A 288 ASP cc_start: 0.7993 (m-30) cc_final: 0.7752 (m-30) REVERT: A 291 LYS cc_start: 0.7780 (ttpp) cc_final: 0.7489 (ttmm) REVERT: A 334 GLU cc_start: 0.6942 (pm20) cc_final: 0.6378 (pp20) REVERT: A 357 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7836 (mt) REVERT: A 360 GLN cc_start: 0.6926 (tt0) cc_final: 0.6547 (tt0) REVERT: B 47 MET cc_start: 0.1462 (OUTLIER) cc_final: 0.0308 (ptm) REVERT: B 83 GLU cc_start: 0.7725 (tt0) cc_final: 0.7196 (mt-10) REVERT: B 176 MET cc_start: 0.8809 (mmm) cc_final: 0.8456 (mmm) REVERT: B 224 GLU cc_start: 0.7516 (tp30) cc_final: 0.6617 (mm-30) REVERT: B 328 LYS cc_start: 0.8035 (tttp) cc_final: 0.7727 (ttpp) REVERT: B 372 ARG cc_start: 0.7015 (mtm-85) cc_final: 0.6713 (mtm180) REVERT: C 25 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7053 (p0) REVERT: C 68 LYS cc_start: 0.8067 (mttm) cc_final: 0.7684 (mtmt) REVERT: C 99 GLU cc_start: 0.7459 (pm20) cc_final: 0.7116 (pm20) REVERT: C 105 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7727 (mp) REVERT: C 276 GLU cc_start: 0.7884 (tt0) cc_final: 0.7324 (mt-10) REVERT: C 328 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7224 (ttmm) REVERT: C 355 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7565 (mmt) REVERT: C 363 ASP cc_start: 0.6991 (m-30) cc_final: 0.6747 (m-30) REVERT: D 72 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: D 298 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7907 (t) REVERT: E 72 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6797 (tt0) REVERT: E 95 ARG cc_start: 0.7131 (mtm-85) cc_final: 0.6579 (mmt90) REVERT: E 128 ASN cc_start: 0.7458 (m110) cc_final: 0.6573 (t0) REVERT: E 178 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7609 (tp) REVERT: E 241 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: E 328 LYS cc_start: 0.7866 (tttt) cc_final: 0.7065 (mttp) REVERT: E 334 GLU cc_start: 0.7625 (pm20) cc_final: 0.7218 (pm20) REVERT: E 351 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7202 (m) REVERT: E 360 GLN cc_start: 0.7284 (tt0) cc_final: 0.6670 (pm20) REVERT: F 72 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7240 (mm-30) REVERT: F 80 ASP cc_start: 0.7745 (m-30) cc_final: 0.7401 (m-30) REVERT: F 95 ARG cc_start: 0.7055 (mtp85) cc_final: 0.6599 (mtt-85) REVERT: F 125 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7585 (mm-30) REVERT: F 167 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8264 (mm-30) REVERT: F 178 LEU cc_start: 0.7950 (tp) cc_final: 0.7417 (mt) REVERT: F 191 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7847 (tmmt) REVERT: F 206 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7217 (ttm110) REVERT: F 326 LYS cc_start: 0.7865 (tppp) cc_final: 0.6642 (ptmm) REVERT: F 328 LYS cc_start: 0.8125 (tttp) cc_final: 0.7698 (tptm) REVERT: F 354 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7314 (mm110) REVERT: F 363 ASP cc_start: 0.7395 (m-30) cc_final: 0.7132 (m-30) REVERT: G 25 ASP cc_start: 0.7145 (m-30) cc_final: 0.6721 (m-30) REVERT: G 95 ARG cc_start: 0.7350 (mtt-85) cc_final: 0.7012 (mtm110) REVERT: G 113 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7693 (mmtp) REVERT: G 118 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7276 (mmmm) REVERT: G 292 ASP cc_start: 0.7914 (m-30) cc_final: 0.7699 (m-30) REVERT: G 326 LYS cc_start: 0.7642 (mmtm) cc_final: 0.6979 (mmtp) REVERT: G 355 MET cc_start: 0.8033 (mmm) cc_final: 0.7766 (mtt) REVERT: H 24 ASP cc_start: 0.6858 (m-30) cc_final: 0.6478 (m-30) REVERT: H 25 ASP cc_start: 0.6753 (p0) cc_final: 0.6239 (p0) REVERT: H 50 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7396 (mtmm) REVERT: H 68 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7914 (mptt) REVERT: H 72 GLU cc_start: 0.7699 (tt0) cc_final: 0.7425 (mp0) REVERT: H 93 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7158 (mm-30) REVERT: H 113 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4603 (mppt) REVERT: H 167 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: H 206 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7295 (ttp-110) REVERT: H 276 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7432 (mt-10) REVERT: H 286 ASP cc_start: 0.6394 (m-30) cc_final: 0.6017 (m-30) REVERT: H 314 GLN cc_start: 0.7588 (tp40) cc_final: 0.7021 (tm130) REVERT: H 326 LYS cc_start: 0.7018 (mmpt) cc_final: 0.6778 (pttm) REVERT: H 328 LYS cc_start: 0.7744 (ttmt) cc_final: 0.7104 (tmtt) REVERT: H 334 GLU cc_start: 0.7760 (pm20) cc_final: 0.6701 (tp30) REVERT: H 336 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7779 (tttm) REVERT: H 354 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6749 (tp-100) REVERT: K 578 ASN cc_start: 0.6544 (t0) cc_final: 0.6290 (t0) REVERT: K 595 LYS cc_start: 0.5878 (mmtp) cc_final: 0.5571 (mmtp) REVERT: K 598 GLU cc_start: 0.6086 (pm20) cc_final: 0.5273 (pt0) REVERT: K 603 MET cc_start: 0.7222 (tpt) cc_final: 0.7003 (tpt) REVERT: K 617 GLU cc_start: 0.6517 (mp0) cc_final: 0.6118 (mt-10) REVERT: K 621 GLU cc_start: 0.7342 (tt0) cc_final: 0.6924 (mt-10) REVERT: L 555 GLU cc_start: 0.7462 (tt0) cc_final: 0.7208 (tt0) REVERT: L 574 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6494 (tp30) REVERT: L 582 LYS cc_start: 0.6347 (mtpt) cc_final: 0.6013 (mttt) REVERT: L 608 GLU cc_start: 0.6936 (tp30) cc_final: 0.6677 (mm-30) REVERT: L 616 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7540 (tmmm) REVERT: M 521 LYS cc_start: 0.6681 (tttp) cc_final: 0.6131 (tttm) REVERT: M 533 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7721 (t) REVERT: M 541 ASP cc_start: 0.7411 (t0) cc_final: 0.6728 (t0) REVERT: M 604 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6076 (tt0) REVERT: M 664 SER cc_start: 0.5231 (t) cc_final: 0.5010 (t) REVERT: N 521 LYS cc_start: 0.7341 (ttpp) cc_final: 0.7101 (ttmm) REVERT: N 528 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7958 (p) REVERT: N 544 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6497 (tp30) REVERT: N 566 ARG cc_start: 0.6367 (ttt180) cc_final: 0.6095 (mtt180) outliers start: 88 outliers final: 39 residues processed: 397 average time/residue: 2.7015 time to fit residues: 1255.2513 Evaluate side-chains 387 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 327 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 528 THR Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 308 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN G 225 ASN H 246 GLN L 534 ASN M 625 GLN N 589 GLN N 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28912 Z= 0.211 Angle : 0.584 7.114 39208 Z= 0.288 Chirality : 0.043 0.167 4344 Planarity : 0.004 0.041 5016 Dihedral : 7.881 119.779 4018 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.58 % Allowed : 12.85 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.80 (0.14), residues: 3536 helix: 0.63 (0.13), residues: 1596 sheet: -0.55 (0.25), residues: 368 loop : 0.98 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.014 0.001 PHE K 568 TYR 0.009 0.001 TYR C 337 ARG 0.005 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 339 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7683 (ptpp) cc_final: 0.7092 (mttp) REVERT: A 81 ASP cc_start: 0.8132 (m-30) cc_final: 0.7746 (m-30) REVERT: A 100 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: A 190 MET cc_start: 0.7774 (ptp) cc_final: 0.7511 (ptm) REVERT: A 191 LYS cc_start: 0.7429 (tttp) cc_final: 0.7160 (tttt) REVERT: A 205 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7050 (mt-10) REVERT: A 221 LEU cc_start: 0.8798 (tp) cc_final: 0.8480 (tm) REVERT: A 224 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6570 (tp30) REVERT: A 227 MET cc_start: 0.8005 (mmt) cc_final: 0.7419 (mmm) REVERT: A 284 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7564 (mttm) REVERT: A 288 ASP cc_start: 0.7944 (m-30) cc_final: 0.7719 (m-30) REVERT: A 291 LYS cc_start: 0.7768 (ttpp) cc_final: 0.7492 (ttmm) REVERT: A 334 GLU cc_start: 0.7015 (pm20) cc_final: 0.6439 (pp20) REVERT: A 357 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 360 GLN cc_start: 0.6936 (tt0) cc_final: 0.6575 (tt0) REVERT: B 47 MET cc_start: 0.1210 (OUTLIER) cc_final: 0.0935 (mmm) REVERT: B 83 GLU cc_start: 0.7741 (tt0) cc_final: 0.7216 (mt-10) REVERT: B 224 GLU cc_start: 0.7540 (tp30) cc_final: 0.6614 (mm-30) REVERT: B 328 LYS cc_start: 0.8035 (tttp) cc_final: 0.7535 (mttp) REVERT: B 372 ARG cc_start: 0.7006 (mtm-85) cc_final: 0.6717 (mtm180) REVERT: C 25 ASP cc_start: 0.7395 (p0) cc_final: 0.7021 (p0) REVERT: C 68 LYS cc_start: 0.8136 (mttm) cc_final: 0.7748 (mtmt) REVERT: C 99 GLU cc_start: 0.7469 (pm20) cc_final: 0.7165 (pm20) REVERT: C 105 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7721 (mp) REVERT: C 276 GLU cc_start: 0.7894 (tt0) cc_final: 0.7349 (mt-10) REVERT: C 328 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7198 (mtmm) REVERT: C 355 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7589 (mmt) REVERT: C 363 ASP cc_start: 0.6949 (m-30) cc_final: 0.6710 (m-30) REVERT: D 72 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: D 95 ARG cc_start: 0.7301 (mtt-85) cc_final: 0.6888 (mmt90) REVERT: D 298 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7920 (t) REVERT: E 72 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6800 (tt0) REVERT: E 95 ARG cc_start: 0.7110 (mtm-85) cc_final: 0.6532 (mmt90) REVERT: E 128 ASN cc_start: 0.7513 (m110) cc_final: 0.6584 (t0) REVERT: E 241 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: E 328 LYS cc_start: 0.7877 (tttt) cc_final: 0.7072 (mttp) REVERT: E 334 GLU cc_start: 0.7625 (pm20) cc_final: 0.7232 (pm20) REVERT: E 351 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7191 (m) REVERT: E 360 GLN cc_start: 0.7260 (tt0) cc_final: 0.6687 (pm20) REVERT: F 72 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7243 (mm-30) REVERT: F 80 ASP cc_start: 0.7691 (m-30) cc_final: 0.7349 (m-30) REVERT: F 95 ARG cc_start: 0.7043 (mtp85) cc_final: 0.6594 (mtt-85) REVERT: F 167 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8278 (mm-30) REVERT: F 178 LEU cc_start: 0.7947 (tp) cc_final: 0.7383 (mt) REVERT: F 191 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7775 (tmtt) REVERT: F 206 ARG cc_start: 0.7602 (ttm110) cc_final: 0.7200 (ttm110) REVERT: F 325 MET cc_start: 0.7828 (mmp) cc_final: 0.7560 (mmp) REVERT: F 326 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.6677 (ptmm) REVERT: F 328 LYS cc_start: 0.8124 (tttp) cc_final: 0.7702 (tptm) REVERT: F 354 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7325 (mm110) REVERT: F 358 THR cc_start: 0.7756 (m) cc_final: 0.7092 (p) REVERT: G 25 ASP cc_start: 0.7181 (m-30) cc_final: 0.6755 (m-30) REVERT: G 95 ARG cc_start: 0.7354 (mtt-85) cc_final: 0.7011 (mtm110) REVERT: G 113 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7671 (mmtp) REVERT: G 118 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7271 (mmmm) REVERT: G 326 LYS cc_start: 0.7609 (mmtm) cc_final: 0.6964 (mmtp) REVERT: G 355 MET cc_start: 0.7993 (mmm) cc_final: 0.7724 (mtt) REVERT: H 24 ASP cc_start: 0.6727 (m-30) cc_final: 0.6338 (m-30) REVERT: H 25 ASP cc_start: 0.6750 (p0) cc_final: 0.6234 (p0) REVERT: H 50 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7402 (mtpm) REVERT: H 68 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7965 (mptt) REVERT: H 72 GLU cc_start: 0.7665 (tt0) cc_final: 0.7396 (mp0) REVERT: H 113 LYS cc_start: 0.5066 (OUTLIER) cc_final: 0.4582 (mppt) REVERT: H 167 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: H 206 ARG cc_start: 0.7673 (ttm110) cc_final: 0.7292 (ttp-110) REVERT: H 276 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7487 (mt-10) REVERT: H 286 ASP cc_start: 0.6424 (m-30) cc_final: 0.6021 (m-30) REVERT: H 314 GLN cc_start: 0.7574 (tp40) cc_final: 0.7029 (tm130) REVERT: H 326 LYS cc_start: 0.6989 (mmpt) cc_final: 0.6768 (pttm) REVERT: H 328 LYS cc_start: 0.7713 (ttmt) cc_final: 0.7078 (tmtt) REVERT: H 334 GLU cc_start: 0.7796 (pm20) cc_final: 0.6742 (tp30) REVERT: H 336 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7778 (tttm) REVERT: H 354 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6929 (tp40) REVERT: K 578 ASN cc_start: 0.6565 (t0) cc_final: 0.6301 (t0) REVERT: K 595 LYS cc_start: 0.5891 (mmtp) cc_final: 0.5575 (mmtp) REVERT: K 598 GLU cc_start: 0.6007 (pm20) cc_final: 0.5364 (pt0) REVERT: K 603 MET cc_start: 0.7257 (tpt) cc_final: 0.7044 (tpt) REVERT: K 617 GLU cc_start: 0.6559 (mp0) cc_final: 0.6159 (mt-10) REVERT: K 621 GLU cc_start: 0.7321 (tt0) cc_final: 0.6882 (mt-10) REVERT: K 629 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6823 (mm-30) REVERT: L 555 GLU cc_start: 0.7470 (tt0) cc_final: 0.7222 (tt0) REVERT: L 574 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6555 (tp30) REVERT: L 582 LYS cc_start: 0.6359 (mtpt) cc_final: 0.5987 (mttt) REVERT: L 616 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7518 (tmmm) REVERT: M 521 LYS cc_start: 0.6681 (tttp) cc_final: 0.6130 (tttm) REVERT: M 527 SER cc_start: 0.8206 (m) cc_final: 0.7863 (p) REVERT: M 533 THR cc_start: 0.7967 (m) cc_final: 0.7729 (t) REVERT: M 541 ASP cc_start: 0.7422 (t0) cc_final: 0.6709 (t0) REVERT: M 604 GLU cc_start: 0.6502 (mm-30) cc_final: 0.5979 (tt0) REVERT: M 625 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6568 (tt0) REVERT: N 521 LYS cc_start: 0.7356 (ttpp) cc_final: 0.7108 (ttmm) REVERT: N 544 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6505 (tp30) REVERT: N 566 ARG cc_start: 0.6350 (ttt180) cc_final: 0.6105 (mtt180) REVERT: N 569 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6043 (m-30) REVERT: N 621 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6496 (mt-10) REVERT: N 629 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6626 (mm-30) outliers start: 78 outliers final: 40 residues processed: 387 average time/residue: 2.6812 time to fit residues: 1207.5027 Evaluate side-chains 378 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 318 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 625 GLN Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 202 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 344 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN G 225 ASN N 589 GLN N 645 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28912 Z= 0.213 Angle : 0.582 7.204 39208 Z= 0.286 Chirality : 0.043 0.166 4344 Planarity : 0.004 0.040 5016 Dihedral : 7.769 118.906 4018 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 2.74 % Allowed : 12.81 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3536 helix: 0.69 (0.13), residues: 1596 sheet: -0.54 (0.25), residues: 368 loop : 1.01 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.013 0.001 PHE B 266 TYR 0.009 0.001 TYR C 337 ARG 0.007 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 325 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7651 (ptpp) cc_final: 0.7100 (mttp) REVERT: A 81 ASP cc_start: 0.8136 (m-30) cc_final: 0.7743 (m-30) REVERT: A 100 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7338 (pt0) REVERT: A 190 MET cc_start: 0.7735 (ptp) cc_final: 0.7514 (ptm) REVERT: A 191 LYS cc_start: 0.7432 (tttp) cc_final: 0.7168 (tttt) REVERT: A 205 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7102 (mt-10) REVERT: A 221 LEU cc_start: 0.8799 (tp) cc_final: 0.8481 (tm) REVERT: A 224 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6566 (tp30) REVERT: A 227 MET cc_start: 0.7996 (mmt) cc_final: 0.7419 (mmm) REVERT: A 284 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7548 (mttm) REVERT: A 291 LYS cc_start: 0.7769 (ttpp) cc_final: 0.7480 (ttmt) REVERT: A 334 GLU cc_start: 0.7008 (pm20) cc_final: 0.6418 (pp20) REVERT: A 357 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7780 (mt) REVERT: B 47 MET cc_start: 0.1188 (OUTLIER) cc_final: 0.0964 (mmm) REVERT: B 83 GLU cc_start: 0.7747 (tt0) cc_final: 0.7241 (mt-10) REVERT: B 224 GLU cc_start: 0.7635 (tp30) cc_final: 0.6625 (mm-30) REVERT: B 328 LYS cc_start: 0.8035 (tttp) cc_final: 0.7557 (mttp) REVERT: B 372 ARG cc_start: 0.7001 (mtm-85) cc_final: 0.6719 (mtm180) REVERT: C 25 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6950 (p0) REVERT: C 68 LYS cc_start: 0.8144 (mttm) cc_final: 0.7756 (mtmt) REVERT: C 99 GLU cc_start: 0.7484 (pm20) cc_final: 0.7167 (pm20) REVERT: C 105 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7723 (mp) REVERT: C 276 GLU cc_start: 0.7892 (tt0) cc_final: 0.7343 (mt-10) REVERT: C 328 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7186 (mtmm) REVERT: C 355 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7617 (mmt) REVERT: C 363 ASP cc_start: 0.6929 (m-30) cc_final: 0.6697 (m-30) REVERT: D 72 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: D 95 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.6883 (mmt90) REVERT: D 298 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (t) REVERT: E 72 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6798 (tt0) REVERT: E 95 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6558 (mmt90) REVERT: E 128 ASN cc_start: 0.7457 (m110) cc_final: 0.6577 (t0) REVERT: E 241 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: E 328 LYS cc_start: 0.7881 (tttt) cc_final: 0.7077 (mttp) REVERT: E 334 GLU cc_start: 0.7609 (pm20) cc_final: 0.7212 (pm20) REVERT: E 351 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7187 (m) REVERT: E 360 GLN cc_start: 0.7295 (tt0) cc_final: 0.6705 (pm20) REVERT: E 373 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7573 (mmmt) REVERT: F 72 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7234 (mm-30) REVERT: F 80 ASP cc_start: 0.7708 (m-30) cc_final: 0.7374 (m-30) REVERT: F 95 ARG cc_start: 0.7018 (mtp85) cc_final: 0.6606 (mtt-85) REVERT: F 125 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7278 (mm-30) REVERT: F 167 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8285 (mm-30) REVERT: F 178 LEU cc_start: 0.7915 (tp) cc_final: 0.7372 (mt) REVERT: F 191 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7897 (tmtt) REVERT: F 206 ARG cc_start: 0.7615 (ttm110) cc_final: 0.7215 (ttm110) REVERT: F 225 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7369 (m-40) REVERT: F 325 MET cc_start: 0.7819 (mmp) cc_final: 0.7494 (mmp) REVERT: F 326 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.6673 (ptmm) REVERT: F 328 LYS cc_start: 0.8133 (tttp) cc_final: 0.7705 (tptm) REVERT: F 354 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7345 (mm110) REVERT: F 358 THR cc_start: 0.7723 (m) cc_final: 0.7135 (p) REVERT: G 25 ASP cc_start: 0.7132 (m-30) cc_final: 0.6709 (m-30) REVERT: G 95 ARG cc_start: 0.7318 (mtt-85) cc_final: 0.6973 (mtm110) REVERT: G 113 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7669 (mmtp) REVERT: G 118 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7276 (mmmm) REVERT: G 269 MET cc_start: 0.8519 (mtp) cc_final: 0.8303 (mtt) REVERT: G 326 LYS cc_start: 0.7596 (mmtm) cc_final: 0.6963 (mmtp) REVERT: G 355 MET cc_start: 0.7988 (mmm) cc_final: 0.7728 (mtt) REVERT: H 24 ASP cc_start: 0.6723 (m-30) cc_final: 0.6330 (m-30) REVERT: H 25 ASP cc_start: 0.6761 (p0) cc_final: 0.6243 (p0) REVERT: H 50 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7387 (mtpm) REVERT: H 68 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7967 (mptt) REVERT: H 72 GLU cc_start: 0.7665 (tt0) cc_final: 0.7394 (mp0) REVERT: H 113 LYS cc_start: 0.5088 (OUTLIER) cc_final: 0.4622 (mppt) REVERT: H 167 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: H 206 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7282 (ttp-110) REVERT: H 276 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7506 (mt-10) REVERT: H 286 ASP cc_start: 0.6385 (m-30) cc_final: 0.5974 (m-30) REVERT: H 314 GLN cc_start: 0.7567 (tp40) cc_final: 0.7028 (tm130) REVERT: H 326 LYS cc_start: 0.6979 (mmpt) cc_final: 0.6764 (pttm) REVERT: H 328 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7106 (tmtt) REVERT: H 334 GLU cc_start: 0.7853 (pm20) cc_final: 0.6732 (tp30) REVERT: H 336 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7819 (ttpt) REVERT: H 354 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6753 (tp-100) REVERT: K 538 MET cc_start: 0.7960 (ttp) cc_final: 0.7528 (ttm) REVERT: K 578 ASN cc_start: 0.6545 (t0) cc_final: 0.6286 (t0) REVERT: K 595 LYS cc_start: 0.5856 (mmtp) cc_final: 0.5574 (mmtp) REVERT: K 598 GLU cc_start: 0.6016 (pm20) cc_final: 0.5380 (pt0) REVERT: K 603 MET cc_start: 0.7318 (tpt) cc_final: 0.7100 (tpt) REVERT: K 617 GLU cc_start: 0.6548 (mp0) cc_final: 0.6149 (mt-10) REVERT: K 621 GLU cc_start: 0.7324 (tt0) cc_final: 0.6910 (mt-10) REVERT: K 629 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6821 (mm-30) REVERT: L 555 GLU cc_start: 0.7486 (tt0) cc_final: 0.7233 (tt0) REVERT: L 574 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6499 (tp30) REVERT: L 582 LYS cc_start: 0.6241 (mtpt) cc_final: 0.5898 (mttt) REVERT: L 616 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7530 (tmmm) REVERT: M 521 LYS cc_start: 0.6698 (tttp) cc_final: 0.6134 (tttm) REVERT: M 527 SER cc_start: 0.8207 (m) cc_final: 0.7861 (p) REVERT: M 533 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7721 (t) REVERT: M 541 ASP cc_start: 0.7445 (t0) cc_final: 0.6743 (t0) REVERT: M 604 GLU cc_start: 0.6486 (mm-30) cc_final: 0.5976 (tt0) REVERT: N 521 LYS cc_start: 0.7416 (ttpp) cc_final: 0.7169 (ttmm) REVERT: N 543 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7019 (ttt90) REVERT: N 544 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6453 (tp30) REVERT: N 566 ARG cc_start: 0.6354 (ttt180) cc_final: 0.6104 (mtt180) REVERT: N 569 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6043 (m-30) outliers start: 83 outliers final: 45 residues processed: 382 average time/residue: 2.7371 time to fit residues: 1222.1635 Evaluate side-chains 387 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 318 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 364 GLU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 533 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 289 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 343 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN G 225 ASN ** M 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 645 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28912 Z= 0.174 Angle : 0.558 7.307 39208 Z= 0.272 Chirality : 0.042 0.166 4344 Planarity : 0.004 0.043 5016 Dihedral : 7.336 111.437 4016 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 2.38 % Allowed : 13.31 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.02 (0.14), residues: 3536 helix: 0.85 (0.14), residues: 1596 sheet: -0.51 (0.24), residues: 368 loop : 1.06 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.008 0.001 HIS A 40 PHE 0.012 0.001 PHE A 255 TYR 0.008 0.001 TYR C 337 ARG 0.008 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 329 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7603 (ptpp) cc_final: 0.7103 (mttp) REVERT: A 81 ASP cc_start: 0.8136 (m-30) cc_final: 0.7742 (m-30) REVERT: A 191 LYS cc_start: 0.7382 (tttp) cc_final: 0.7130 (tttt) REVERT: A 205 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 221 LEU cc_start: 0.8801 (tp) cc_final: 0.8495 (tm) REVERT: A 224 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6587 (tp30) REVERT: A 227 MET cc_start: 0.7960 (mmt) cc_final: 0.7399 (mmm) REVERT: A 284 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7515 (mttm) REVERT: A 288 ASP cc_start: 0.7930 (m-30) cc_final: 0.7681 (m-30) REVERT: A 291 LYS cc_start: 0.7751 (ttpp) cc_final: 0.7482 (ttmt) REVERT: A 299 MET cc_start: 0.8232 (mmt) cc_final: 0.7804 (mtp) REVERT: A 334 GLU cc_start: 0.6964 (pm20) cc_final: 0.6355 (pp20) REVERT: A 357 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7805 (mt) REVERT: B 83 GLU cc_start: 0.7753 (tt0) cc_final: 0.7188 (mt-10) REVERT: B 224 GLU cc_start: 0.7626 (tp30) cc_final: 0.6611 (mm-30) REVERT: B 328 LYS cc_start: 0.7997 (tttp) cc_final: 0.7556 (mttp) REVERT: B 334 GLU cc_start: 0.7068 (pm20) cc_final: 0.6800 (pp20) REVERT: B 364 GLU cc_start: 0.6783 (tt0) cc_final: 0.6564 (mt-10) REVERT: B 372 ARG cc_start: 0.7044 (mtm-85) cc_final: 0.6744 (mtm180) REVERT: C 25 ASP cc_start: 0.7439 (p0) cc_final: 0.6976 (p0) REVERT: C 68 LYS cc_start: 0.8104 (mttm) cc_final: 0.7725 (mtmt) REVERT: C 99 GLU cc_start: 0.7483 (pm20) cc_final: 0.7122 (pm20) REVERT: C 105 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7697 (mp) REVERT: C 276 GLU cc_start: 0.7851 (tt0) cc_final: 0.7303 (mt-10) REVERT: C 328 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7192 (mtmm) REVERT: C 363 ASP cc_start: 0.6922 (m-30) cc_final: 0.6704 (m-30) REVERT: D 72 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: D 95 ARG cc_start: 0.7250 (mtt-85) cc_final: 0.6847 (mmt90) REVERT: D 298 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7859 (t) REVERT: E 72 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6732 (tt0) REVERT: E 95 ARG cc_start: 0.7106 (mtm-85) cc_final: 0.6542 (mmt90) REVERT: E 128 ASN cc_start: 0.7468 (m110) cc_final: 0.6613 (t0) REVERT: E 179 ASP cc_start: 0.7569 (m-30) cc_final: 0.7350 (m-30) REVERT: E 241 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: E 328 LYS cc_start: 0.7858 (tttt) cc_final: 0.7076 (mttp) REVERT: E 334 GLU cc_start: 0.7621 (pm20) cc_final: 0.7198 (pm20) REVERT: E 351 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7177 (m) REVERT: E 360 GLN cc_start: 0.7291 (tt0) cc_final: 0.6706 (pm20) REVERT: E 373 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7579 (mmmt) REVERT: F 72 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7228 (mm-30) REVERT: F 80 ASP cc_start: 0.7683 (m-30) cc_final: 0.7360 (m-30) REVERT: F 95 ARG cc_start: 0.7009 (mtp85) cc_final: 0.6604 (mtt-85) REVERT: F 167 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8287 (mm-30) REVERT: F 178 LEU cc_start: 0.7868 (tp) cc_final: 0.7361 (mt) REVERT: F 206 ARG cc_start: 0.7592 (ttm110) cc_final: 0.7223 (ttm110) REVERT: F 225 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7423 (m-40) REVERT: F 226 GLU cc_start: 0.7962 (tp30) cc_final: 0.7758 (tp30) REVERT: F 325 MET cc_start: 0.7831 (mmp) cc_final: 0.7510 (mmp) REVERT: F 326 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.6686 (ptmm) REVERT: F 328 LYS cc_start: 0.8134 (tttp) cc_final: 0.7709 (tptm) REVERT: F 354 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7350 (mm110) REVERT: F 358 THR cc_start: 0.7707 (m) cc_final: 0.7114 (p) REVERT: G 25 ASP cc_start: 0.7133 (m-30) cc_final: 0.6709 (m-30) REVERT: G 95 ARG cc_start: 0.7332 (mtt-85) cc_final: 0.6987 (mtm110) REVERT: G 113 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7681 (mmtp) REVERT: G 118 LYS cc_start: 0.7811 (mmmt) cc_final: 0.7290 (mmmm) REVERT: G 123 MET cc_start: 0.8450 (mmp) cc_final: 0.8172 (mmp) REVERT: G 269 MET cc_start: 0.8487 (mtp) cc_final: 0.8242 (mtt) REVERT: G 326 LYS cc_start: 0.7591 (mmtm) cc_final: 0.6969 (mmtp) REVERT: H 24 ASP cc_start: 0.6723 (m-30) cc_final: 0.6331 (m-30) REVERT: H 25 ASP cc_start: 0.6772 (p0) cc_final: 0.6260 (p0) REVERT: H 50 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7311 (mtpm) REVERT: H 68 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7980 (mptt) REVERT: H 72 GLU cc_start: 0.7651 (tt0) cc_final: 0.7382 (mp0) REVERT: H 113 LYS cc_start: 0.5009 (OUTLIER) cc_final: 0.3930 (mmtm) REVERT: H 167 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: H 276 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7484 (mt-10) REVERT: H 286 ASP cc_start: 0.6333 (m-30) cc_final: 0.5939 (m-30) REVERT: H 305 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8108 (tpt) REVERT: H 314 GLN cc_start: 0.7487 (tp40) cc_final: 0.6982 (tm130) REVERT: H 326 LYS cc_start: 0.6999 (mmpt) cc_final: 0.6797 (pttm) REVERT: H 328 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7067 (tmtt) REVERT: H 334 GLU cc_start: 0.7829 (pm20) cc_final: 0.6652 (tp30) REVERT: H 336 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7853 (ttpt) REVERT: H 354 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6754 (tp-100) REVERT: K 574 GLU cc_start: 0.7184 (tt0) cc_final: 0.6884 (tp30) REVERT: K 578 ASN cc_start: 0.6481 (t0) cc_final: 0.6211 (t0) REVERT: K 595 LYS cc_start: 0.5892 (mmtp) cc_final: 0.5577 (mmtp) REVERT: K 598 GLU cc_start: 0.6019 (pm20) cc_final: 0.5383 (pt0) REVERT: K 608 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6234 (mm-30) REVERT: K 617 GLU cc_start: 0.6521 (mp0) cc_final: 0.6147 (mt-10) REVERT: K 621 GLU cc_start: 0.7302 (tt0) cc_final: 0.6893 (mt-10) REVERT: K 629 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6877 (mm-30) REVERT: L 555 GLU cc_start: 0.7493 (tt0) cc_final: 0.7222 (tt0) REVERT: L 582 LYS cc_start: 0.6214 (mtpt) cc_final: 0.5876 (mttt) REVERT: L 595 LYS cc_start: 0.6558 (ptpt) cc_final: 0.5933 (mtmt) REVERT: L 616 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7506 (tmmm) REVERT: M 521 LYS cc_start: 0.6693 (tttp) cc_final: 0.6138 (tttt) REVERT: M 527 SER cc_start: 0.8215 (m) cc_final: 0.7855 (p) REVERT: M 533 THR cc_start: 0.7954 (m) cc_final: 0.7701 (t) REVERT: M 541 ASP cc_start: 0.7471 (t0) cc_final: 0.6761 (t0) REVERT: M 589 GLN cc_start: 0.6395 (tt0) cc_final: 0.6171 (tt0) REVERT: M 604 GLU cc_start: 0.6415 (mm-30) cc_final: 0.5924 (tt0) REVERT: N 521 LYS cc_start: 0.7402 (ttpp) cc_final: 0.7152 (ttmm) REVERT: N 543 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7107 (ttt90) REVERT: N 566 ARG cc_start: 0.6310 (ttt180) cc_final: 0.6063 (mtt180) REVERT: N 569 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6047 (m-30) outliers start: 72 outliers final: 44 residues processed: 378 average time/residue: 2.7411 time to fit residues: 1210.9114 Evaluate side-chains 379 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 317 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 616 LYS Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 664 SER Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN E 137 GLN F 162 ASN G 225 ASN K 645 ASN N 589 GLN N 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28912 Z= 0.294 Angle : 0.620 7.486 39208 Z= 0.307 Chirality : 0.044 0.174 4344 Planarity : 0.004 0.041 5016 Dihedral : 7.937 121.970 4016 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 2.48 % Allowed : 13.41 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3536 helix: 0.64 (0.13), residues: 1596 sheet: -0.59 (0.24), residues: 368 loop : 0.93 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 340 HIS 0.008 0.001 HIS A 40 PHE 0.024 0.002 PHE B 266 TYR 0.011 0.001 TYR K 665 ARG 0.007 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 314 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7764 (ptpp) cc_final: 0.7141 (mttp) REVERT: A 81 ASP cc_start: 0.8133 (m-30) cc_final: 0.7763 (m-30) REVERT: A 191 LYS cc_start: 0.7479 (tttp) cc_final: 0.7195 (tttt) REVERT: A 205 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 221 LEU cc_start: 0.8845 (tp) cc_final: 0.8550 (tm) REVERT: A 224 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6473 (tp30) REVERT: A 227 MET cc_start: 0.7991 (mmt) cc_final: 0.7406 (mmm) REVERT: A 284 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7590 (mttm) REVERT: A 291 LYS cc_start: 0.7744 (ttpp) cc_final: 0.7473 (ttmt) REVERT: A 334 GLU cc_start: 0.6965 (pm20) cc_final: 0.6367 (pp20) REVERT: A 357 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7768 (mt) REVERT: B 83 GLU cc_start: 0.7751 (tt0) cc_final: 0.7228 (mt-10) REVERT: B 224 GLU cc_start: 0.7669 (tp30) cc_final: 0.6677 (mm-30) REVERT: B 328 LYS cc_start: 0.8046 (tttp) cc_final: 0.7729 (ttpp) REVERT: B 372 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6782 (mtm180) REVERT: C 25 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6965 (p0) REVERT: C 68 LYS cc_start: 0.8152 (mttm) cc_final: 0.7767 (mtmt) REVERT: C 99 GLU cc_start: 0.7454 (pm20) cc_final: 0.7150 (pm20) REVERT: C 105 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7689 (mp) REVERT: C 276 GLU cc_start: 0.7825 (tt0) cc_final: 0.7297 (mt-10) REVERT: C 328 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7168 (mtmm) REVERT: C 363 ASP cc_start: 0.6938 (m-30) cc_final: 0.6720 (m-30) REVERT: D 72 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: D 95 ARG cc_start: 0.7303 (mtt-85) cc_final: 0.6901 (mmt90) REVERT: D 298 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7931 (t) REVERT: E 72 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6810 (tt0) REVERT: E 95 ARG cc_start: 0.7102 (mtm-85) cc_final: 0.6545 (mmt90) REVERT: E 128 ASN cc_start: 0.7511 (m110) cc_final: 0.6569 (t0) REVERT: E 241 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: E 328 LYS cc_start: 0.7890 (tttt) cc_final: 0.7057 (mttp) REVERT: E 334 GLU cc_start: 0.7657 (pm20) cc_final: 0.7227 (pm20) REVERT: E 351 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7304 (m) REVERT: E 360 GLN cc_start: 0.7295 (tt0) cc_final: 0.6695 (pm20) REVERT: E 373 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7561 (mmmt) REVERT: F 72 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7226 (mm-30) REVERT: F 80 ASP cc_start: 0.7677 (m-30) cc_final: 0.7414 (m-30) REVERT: F 95 ARG cc_start: 0.7043 (mtp85) cc_final: 0.6689 (mtt-85) REVERT: F 167 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8306 (mm-30) REVERT: F 178 LEU cc_start: 0.7881 (tp) cc_final: 0.7385 (mt) REVERT: F 191 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7874 (tmtt) REVERT: F 206 ARG cc_start: 0.7603 (ttm110) cc_final: 0.7244 (ttm110) REVERT: F 326 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.6663 (ptmm) REVERT: F 328 LYS cc_start: 0.8082 (tttp) cc_final: 0.7656 (tptm) REVERT: F 354 GLN cc_start: 0.7660 (mm-40) cc_final: 0.7341 (mm110) REVERT: F 358 THR cc_start: 0.7724 (m) cc_final: 0.7146 (p) REVERT: G 25 ASP cc_start: 0.7147 (m-30) cc_final: 0.6733 (m-30) REVERT: G 118 LYS cc_start: 0.7800 (mmmt) cc_final: 0.7275 (mmmm) REVERT: G 269 MET cc_start: 0.8481 (mtp) cc_final: 0.8272 (mtt) REVERT: G 326 LYS cc_start: 0.7606 (mmtm) cc_final: 0.6971 (mmtp) REVERT: H 24 ASP cc_start: 0.6792 (m-30) cc_final: 0.6396 (m-30) REVERT: H 25 ASP cc_start: 0.6792 (p0) cc_final: 0.6306 (p0) REVERT: H 50 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7390 (mtpm) REVERT: H 68 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7937 (mptt) REVERT: H 72 GLU cc_start: 0.7756 (tt0) cc_final: 0.7428 (mp0) REVERT: H 113 LYS cc_start: 0.5008 (OUTLIER) cc_final: 0.3863 (mmtm) REVERT: H 167 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: H 176 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7580 (mtm) REVERT: H 276 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7521 (mt-10) REVERT: H 286 ASP cc_start: 0.6268 (m-30) cc_final: 0.5869 (m-30) REVERT: H 326 LYS cc_start: 0.7021 (mmpt) cc_final: 0.6808 (pttm) REVERT: H 328 LYS cc_start: 0.7695 (ttmt) cc_final: 0.6975 (tmtt) REVERT: H 334 GLU cc_start: 0.7880 (pm20) cc_final: 0.6733 (tp30) REVERT: H 336 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7814 (ttpt) REVERT: H 354 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6771 (tp-100) REVERT: K 538 MET cc_start: 0.7962 (ttp) cc_final: 0.7528 (ttm) REVERT: K 578 ASN cc_start: 0.6495 (t0) cc_final: 0.6255 (t0) REVERT: K 598 GLU cc_start: 0.6068 (pm20) cc_final: 0.5450 (pt0) REVERT: K 621 GLU cc_start: 0.7322 (tt0) cc_final: 0.6909 (mt-10) REVERT: K 629 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6915 (mm-30) REVERT: L 555 GLU cc_start: 0.7454 (tt0) cc_final: 0.7190 (tt0) REVERT: L 582 LYS cc_start: 0.6276 (mtpt) cc_final: 0.5874 (mmtp) REVERT: M 521 LYS cc_start: 0.6672 (tttp) cc_final: 0.6182 (tttm) REVERT: M 533 THR cc_start: 0.7981 (m) cc_final: 0.7718 (t) REVERT: M 589 GLN cc_start: 0.6421 (tt0) cc_final: 0.6173 (tt0) REVERT: M 604 GLU cc_start: 0.6485 (mm-30) cc_final: 0.5968 (tt0) REVERT: M 653 ASP cc_start: 0.5942 (m-30) cc_final: 0.5700 (p0) REVERT: N 521 LYS cc_start: 0.7479 (ttpp) cc_final: 0.7256 (ttmm) REVERT: N 543 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6920 (ttt90) REVERT: N 566 ARG cc_start: 0.6340 (ttt180) cc_final: 0.6045 (mtt180) REVERT: N 569 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6058 (m-30) outliers start: 75 outliers final: 46 residues processed: 368 average time/residue: 2.7028 time to fit residues: 1155.6875 Evaluate side-chains 372 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 308 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 664 SER Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 0.5980 chunk 328 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 319 optimal weight: 0.6980 chunk 192 optimal weight: 0.0670 chunk 139 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN E 137 GLN G 225 ASN ** M 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 589 GLN N 645 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28912 Z= 0.199 Angle : 0.577 7.045 39208 Z= 0.282 Chirality : 0.042 0.168 4344 Planarity : 0.004 0.043 5016 Dihedral : 7.491 117.408 4013 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 2.34 % Allowed : 13.67 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3536 helix: 0.76 (0.13), residues: 1596 sheet: -0.53 (0.25), residues: 368 loop : 0.99 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.013 0.001 PHE K 568 TYR 0.010 0.001 TYR C 337 ARG 0.008 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 313 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7766 (ptpp) cc_final: 0.7131 (mttp) REVERT: A 81 ASP cc_start: 0.8118 (m-30) cc_final: 0.7748 (m-30) REVERT: A 205 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7090 (mt-10) REVERT: A 221 LEU cc_start: 0.8808 (tp) cc_final: 0.8522 (tm) REVERT: A 224 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6508 (tp30) REVERT: A 227 MET cc_start: 0.7956 (mmt) cc_final: 0.7385 (mmm) REVERT: A 284 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7573 (mttm) REVERT: A 291 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7470 (ttmt) REVERT: A 334 GLU cc_start: 0.6913 (pm20) cc_final: 0.6284 (pp20) REVERT: A 357 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7742 (mt) REVERT: B 83 GLU cc_start: 0.7776 (tt0) cc_final: 0.7224 (mt-10) REVERT: B 224 GLU cc_start: 0.7658 (tp30) cc_final: 0.6653 (mm-30) REVERT: B 328 LYS cc_start: 0.8026 (tttp) cc_final: 0.7569 (mttp) REVERT: B 372 ARG cc_start: 0.7070 (mtm-85) cc_final: 0.6777 (mtm180) REVERT: C 25 ASP cc_start: 0.7404 (p0) cc_final: 0.6952 (p0) REVERT: C 68 LYS cc_start: 0.8137 (mttm) cc_final: 0.7751 (mtmt) REVERT: C 99 GLU cc_start: 0.7465 (pm20) cc_final: 0.7148 (pm20) REVERT: C 105 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7688 (mp) REVERT: C 276 GLU cc_start: 0.7808 (tt0) cc_final: 0.7283 (mt-10) REVERT: C 328 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7140 (mtmm) REVERT: C 363 ASP cc_start: 0.6927 (m-30) cc_final: 0.6711 (m-30) REVERT: D 72 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: D 95 ARG cc_start: 0.7256 (mtt-85) cc_final: 0.6856 (mmt90) REVERT: D 298 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7905 (t) REVERT: E 72 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6765 (tt0) REVERT: E 95 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6544 (mmt90) REVERT: E 128 ASN cc_start: 0.7453 (m110) cc_final: 0.6594 (t0) REVERT: E 178 LEU cc_start: 0.7924 (mt) cc_final: 0.7496 (mt) REVERT: E 241 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: E 328 LYS cc_start: 0.7889 (tttt) cc_final: 0.7060 (mttp) REVERT: E 334 GLU cc_start: 0.7666 (pm20) cc_final: 0.7282 (pm20) REVERT: E 351 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7302 (m) REVERT: E 360 GLN cc_start: 0.7300 (tt0) cc_final: 0.6698 (pm20) REVERT: E 373 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7580 (mmmt) REVERT: F 72 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7224 (mm-30) REVERT: F 80 ASP cc_start: 0.7745 (m-30) cc_final: 0.7463 (m-30) REVERT: F 95 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6606 (mtt-85) REVERT: F 167 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8296 (mm-30) REVERT: F 178 LEU cc_start: 0.7832 (tp) cc_final: 0.7354 (mt) REVERT: F 191 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7869 (tmtt) REVERT: F 206 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7250 (ttm110) REVERT: F 225 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7359 (m-40) REVERT: F 326 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.6663 (ptmm) REVERT: F 328 LYS cc_start: 0.8111 (tttp) cc_final: 0.7694 (tptm) REVERT: F 354 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7345 (mm110) REVERT: F 358 THR cc_start: 0.7722 (m) cc_final: 0.7143 (p) REVERT: G 25 ASP cc_start: 0.7134 (m-30) cc_final: 0.6722 (m-30) REVERT: G 113 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7676 (mmtp) REVERT: G 118 LYS cc_start: 0.7818 (mmmt) cc_final: 0.7287 (mmmm) REVERT: G 123 MET cc_start: 0.8445 (mmp) cc_final: 0.8176 (mmp) REVERT: G 269 MET cc_start: 0.8503 (mtp) cc_final: 0.8270 (mtt) REVERT: G 326 LYS cc_start: 0.7594 (mmtm) cc_final: 0.6967 (mmtp) REVERT: H 24 ASP cc_start: 0.6717 (m-30) cc_final: 0.6322 (m-30) REVERT: H 25 ASP cc_start: 0.6786 (p0) cc_final: 0.6302 (p0) REVERT: H 50 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7387 (mtpm) REVERT: H 68 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7940 (mptt) REVERT: H 72 GLU cc_start: 0.7738 (tt0) cc_final: 0.7415 (mp0) REVERT: H 113 LYS cc_start: 0.5052 (OUTLIER) cc_final: 0.3918 (mmtm) REVERT: H 176 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7626 (mtm) REVERT: H 276 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7523 (mt-10) REVERT: H 286 ASP cc_start: 0.6190 (m-30) cc_final: 0.5817 (m-30) REVERT: H 326 LYS cc_start: 0.7032 (mmpt) cc_final: 0.6777 (pttm) REVERT: H 328 LYS cc_start: 0.7590 (ttmt) cc_final: 0.7140 (tmtt) REVERT: H 334 GLU cc_start: 0.7862 (pm20) cc_final: 0.6724 (tp30) REVERT: H 336 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7779 (tttm) REVERT: H 354 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6787 (tp-100) REVERT: K 538 MET cc_start: 0.7956 (ttp) cc_final: 0.7550 (ttm) REVERT: K 574 GLU cc_start: 0.7204 (tt0) cc_final: 0.6885 (tp30) REVERT: K 578 ASN cc_start: 0.6492 (t0) cc_final: 0.6239 (t0) REVERT: K 598 GLU cc_start: 0.6039 (pm20) cc_final: 0.5420 (pt0) REVERT: K 621 GLU cc_start: 0.7320 (tt0) cc_final: 0.6907 (mt-10) REVERT: K 629 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6894 (mm-30) REVERT: L 555 GLU cc_start: 0.7431 (tt0) cc_final: 0.7168 (tt0) REVERT: L 582 LYS cc_start: 0.6287 (mtpt) cc_final: 0.5907 (mmtp) REVERT: M 521 LYS cc_start: 0.6659 (tttp) cc_final: 0.6133 (tttt) REVERT: M 527 SER cc_start: 0.8198 (m) cc_final: 0.7850 (p) REVERT: M 533 THR cc_start: 0.7947 (m) cc_final: 0.7695 (t) REVERT: M 541 ASP cc_start: 0.7386 (t0) cc_final: 0.6703 (t0) REVERT: M 589 GLN cc_start: 0.6403 (tt0) cc_final: 0.6171 (tt0) REVERT: M 604 GLU cc_start: 0.6419 (mm-30) cc_final: 0.5930 (tt0) REVERT: M 653 ASP cc_start: 0.5839 (m-30) cc_final: 0.5614 (p0) REVERT: N 521 LYS cc_start: 0.7480 (ttpp) cc_final: 0.7244 (ttmm) REVERT: N 543 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7101 (ttt90) REVERT: N 566 ARG cc_start: 0.6312 (ttt180) cc_final: 0.6029 (mtt180) REVERT: N 569 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6049 (m-30) REVERT: N 608 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5866 (tp30) outliers start: 71 outliers final: 45 residues processed: 364 average time/residue: 2.7355 time to fit residues: 1166.5042 Evaluate side-chains 372 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 309 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 664 SER Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 608 GLU Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.9980 chunk 338 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 326 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN G 225 ASN ** M 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 589 GLN N 645 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28912 Z= 0.200 Angle : 0.574 7.064 39208 Z= 0.281 Chirality : 0.042 0.165 4344 Planarity : 0.004 0.044 5016 Dihedral : 7.357 115.652 4013 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 2.11 % Allowed : 13.97 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.99 (0.14), residues: 3536 helix: 0.84 (0.14), residues: 1548 sheet: -0.49 (0.25), residues: 368 loop : 1.01 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.016 0.001 PHE B 266 TYR 0.009 0.001 TYR C 337 ARG 0.009 0.000 ARG F 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 314 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7726 (ptpp) cc_final: 0.7129 (mttp) REVERT: A 81 ASP cc_start: 0.8123 (m-30) cc_final: 0.7762 (m-30) REVERT: A 205 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6974 (mt-10) REVERT: A 221 LEU cc_start: 0.8808 (tp) cc_final: 0.8521 (tm) REVERT: A 224 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6530 (tp30) REVERT: A 227 MET cc_start: 0.7952 (mmt) cc_final: 0.7381 (mmm) REVERT: A 284 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7571 (mttm) REVERT: A 291 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7465 (ttmt) REVERT: A 334 GLU cc_start: 0.6922 (pm20) cc_final: 0.6289 (pp20) REVERT: A 357 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 83 GLU cc_start: 0.7808 (tt0) cc_final: 0.7262 (mt-10) REVERT: B 224 GLU cc_start: 0.7665 (tp30) cc_final: 0.6668 (mm-30) REVERT: B 328 LYS cc_start: 0.8041 (tttp) cc_final: 0.7579 (mttp) REVERT: B 334 GLU cc_start: 0.7067 (pm20) cc_final: 0.6803 (pp20) REVERT: B 364 GLU cc_start: 0.6889 (tt0) cc_final: 0.6597 (mt-10) REVERT: B 372 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6771 (mtm180) REVERT: C 25 ASP cc_start: 0.7375 (p0) cc_final: 0.6923 (p0) REVERT: C 68 LYS cc_start: 0.8126 (mttm) cc_final: 0.7746 (mtmt) REVERT: C 99 GLU cc_start: 0.7467 (pm20) cc_final: 0.7148 (pm20) REVERT: C 105 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7686 (mp) REVERT: C 276 GLU cc_start: 0.7807 (tt0) cc_final: 0.7285 (mt-10) REVERT: C 328 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7143 (mtmm) REVERT: C 363 ASP cc_start: 0.6939 (m-30) cc_final: 0.6733 (m-30) REVERT: D 72 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: D 95 ARG cc_start: 0.7251 (mtt-85) cc_final: 0.6856 (mmt90) REVERT: D 298 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7890 (t) REVERT: E 72 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6730 (tt0) REVERT: E 95 ARG cc_start: 0.7111 (mtm-85) cc_final: 0.6551 (mmt90) REVERT: E 128 ASN cc_start: 0.7457 (m110) cc_final: 0.6607 (t0) REVERT: E 178 LEU cc_start: 0.7996 (mt) cc_final: 0.7582 (mt) REVERT: E 241 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: E 328 LYS cc_start: 0.7885 (tttt) cc_final: 0.7050 (mttp) REVERT: E 334 GLU cc_start: 0.7663 (pm20) cc_final: 0.7275 (pm20) REVERT: E 351 THR cc_start: 0.7617 (OUTLIER) cc_final: 0.7302 (m) REVERT: E 360 GLN cc_start: 0.7301 (tt0) cc_final: 0.6699 (pm20) REVERT: E 373 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7591 (mmmt) REVERT: F 72 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7220 (mm-30) REVERT: F 80 ASP cc_start: 0.7749 (m-30) cc_final: 0.7467 (m-30) REVERT: F 95 ARG cc_start: 0.7013 (mtp85) cc_final: 0.6567 (mtt-85) REVERT: F 167 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8295 (mm-30) REVERT: F 178 LEU cc_start: 0.7822 (tp) cc_final: 0.7375 (mt) REVERT: F 191 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7874 (tmtt) REVERT: F 206 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7224 (ttm110) REVERT: F 225 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7363 (m-40) REVERT: F 326 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.6662 (ptmm) REVERT: F 328 LYS cc_start: 0.8125 (tttp) cc_final: 0.7718 (tptm) REVERT: F 354 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7291 (mm110) REVERT: F 358 THR cc_start: 0.7719 (m) cc_final: 0.7201 (p) REVERT: G 25 ASP cc_start: 0.7128 (m-30) cc_final: 0.6720 (m-30) REVERT: G 113 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7671 (mmtp) REVERT: G 118 LYS cc_start: 0.7822 (mmmt) cc_final: 0.7288 (mmmm) REVERT: G 269 MET cc_start: 0.8506 (mtp) cc_final: 0.8266 (mtt) REVERT: G 326 LYS cc_start: 0.7595 (mmtm) cc_final: 0.6972 (mmtp) REVERT: H 24 ASP cc_start: 0.6716 (m-30) cc_final: 0.6325 (m-30) REVERT: H 25 ASP cc_start: 0.6796 (p0) cc_final: 0.6314 (p0) REVERT: H 50 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7384 (mtpm) REVERT: H 68 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7946 (mptt) REVERT: H 72 GLU cc_start: 0.7739 (tt0) cc_final: 0.7415 (mp0) REVERT: H 113 LYS cc_start: 0.5035 (OUTLIER) cc_final: 0.3940 (mmtm) REVERT: H 276 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7524 (mt-10) REVERT: H 286 ASP cc_start: 0.6117 (m-30) cc_final: 0.5736 (m-30) REVERT: H 314 GLN cc_start: 0.7658 (tt0) cc_final: 0.6924 (tm130) REVERT: H 326 LYS cc_start: 0.6997 (mmpt) cc_final: 0.6794 (pttm) REVERT: H 328 LYS cc_start: 0.7701 (ttmt) cc_final: 0.7159 (tmtt) REVERT: H 334 GLU cc_start: 0.7889 (pm20) cc_final: 0.6765 (tp30) REVERT: H 336 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7768 (tttm) REVERT: H 354 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6758 (tp-100) REVERT: K 538 MET cc_start: 0.7951 (ttp) cc_final: 0.7537 (ttm) REVERT: K 574 GLU cc_start: 0.7210 (tt0) cc_final: 0.6886 (tp30) REVERT: K 578 ASN cc_start: 0.6482 (t0) cc_final: 0.6233 (t0) REVERT: K 598 GLU cc_start: 0.6001 (pm20) cc_final: 0.5431 (pt0) REVERT: K 621 GLU cc_start: 0.7323 (tt0) cc_final: 0.6919 (mt-10) REVERT: L 555 GLU cc_start: 0.7397 (tt0) cc_final: 0.7132 (tt0) REVERT: L 574 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6946 (tm-30) REVERT: L 582 LYS cc_start: 0.6221 (mtpt) cc_final: 0.5964 (mttt) REVERT: M 521 LYS cc_start: 0.6612 (tttp) cc_final: 0.6102 (tttt) REVERT: M 527 SER cc_start: 0.8200 (m) cc_final: 0.7849 (p) REVERT: M 533 THR cc_start: 0.7944 (m) cc_final: 0.7696 (t) REVERT: M 541 ASP cc_start: 0.7366 (t0) cc_final: 0.6677 (t0) REVERT: M 589 GLN cc_start: 0.6523 (tt0) cc_final: 0.6292 (tt0) REVERT: M 604 GLU cc_start: 0.6417 (mm-30) cc_final: 0.5928 (tt0) REVERT: M 653 ASP cc_start: 0.5881 (m-30) cc_final: 0.5656 (p0) REVERT: N 521 LYS cc_start: 0.7422 (ttpp) cc_final: 0.7177 (ttmm) REVERT: N 543 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7101 (ttt90) REVERT: N 566 ARG cc_start: 0.6309 (ttt180) cc_final: 0.6024 (mtt180) REVERT: N 569 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6050 (m-30) REVERT: N 608 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5860 (tp30) outliers start: 64 outliers final: 44 residues processed: 362 average time/residue: 2.6810 time to fit residues: 1130.3701 Evaluate side-chains 370 residues out of total 3028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 309 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 225 ASN Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 354 GLN Chi-restraints excluded: chain K residue 527 SER Chi-restraints excluded: chain K residue 642 VAL Chi-restraints excluded: chain K residue 655 SER Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain L residue 663 GLU Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 559 SER Chi-restraints excluded: chain M residue 611 THR Chi-restraints excluded: chain M residue 664 SER Chi-restraints excluded: chain N residue 543 ARG Chi-restraints excluded: chain N residue 569 ASP Chi-restraints excluded: chain N residue 580 THR Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 608 GLU Chi-restraints excluded: chain N residue 611 THR Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.9980 chunk 300 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 290 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN G 225 ASN ** M 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 589 GLN N 645 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085058 restraints weight = 113079.821| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.14 r_work: 0.2893 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28912 Z= 0.247 Angle : 0.598 6.885 39208 Z= 0.295 Chirality : 0.043 0.163 4344 Planarity : 0.004 0.042 5016 Dihedral : 7.567 118.950 4012 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 2.18 % Allowed : 14.04 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3536 helix: 0.76 (0.14), residues: 1548 sheet: -0.54 (0.24), residues: 368 loop : 0.95 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.007 0.001 HIS A 40 PHE 0.016 0.002 PHE B 266 TYR 0.010 0.001 TYR A 166 ARG 0.009 0.000 ARG F 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18074.38 seconds wall clock time: 311 minutes 23.74 seconds (18683.74 seconds total)