Starting phenix.real_space_refine (version: dev) on Tue Feb 21 20:21:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qim_13990/02_2023/7qim_13990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qim_13990/02_2023/7qim_13990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qim_13990/02_2023/7qim_13990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qim_13990/02_2023/7qim_13990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qim_13990/02_2023/7qim_13990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qim_13990/02_2023/7qim_13990_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "C ARG 39": "NH1" <-> "NH2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15550 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 546 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 364 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'UNK:plan-1': 68} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.15, per 1000 atoms: 0.59 Number of scatterers: 15550 At special positions: 0 Unit cell: (102.07, 89.96, 197.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2995 8.00 N 2645 7.00 C 9790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.21 Conformation dependent library (CDL) restraints added in 2.3 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 25 sheets defined 51.5% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 79 through 94 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 195 removed outlier: 3.597A pdb=" N MET C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.551A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 210 " --> pdb=" O ARG C 206 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.949A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.605A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 262' Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 288 through 295 removed outlier: 4.019A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 304 No H-bonds generated for 'chain 'C' and resid 301 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.020A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 79 through 94 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 195 removed outlier: 3.598A pdb=" N MET B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.551A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.950A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix removed outlier: 4.605A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 262' Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 288 through 295 removed outlier: 4.019A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 304 No H-bonds generated for 'chain 'B' and resid 301 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.019A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 79 through 94 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.598A pdb=" N MET A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.551A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.950A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 258 - end of helix removed outlier: 4.605A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 262' Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 288 through 295 removed outlier: 4.019A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 304 No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.019A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 79 through 94 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 195 removed outlier: 3.598A pdb=" N MET D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.551A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.949A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Proline residue: D 258 - end of helix removed outlier: 4.605A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 262' Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 288 through 295 removed outlier: 4.020A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 304 No H-bonds generated for 'chain 'D' and resid 301 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.019A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 367 through 373 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 79 through 94 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 195 removed outlier: 3.598A pdb=" N MET E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.550A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 210 " --> pdb=" O ARG E 206 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 253 through 262 removed outlier: 3.949A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix removed outlier: 4.606A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 262' Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 288 through 295 removed outlier: 4.019A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.019A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 367 through 373 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.686A pdb=" N UNK F 29 " --> pdb=" O UNK F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 52 removed outlier: 3.676A pdb=" N UNK F 45 " --> pdb=" O UNK F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 65 removed outlier: 3.822A pdb=" N UNK F 59 " --> pdb=" O UNK F 55 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N UNK F 61 " --> pdb=" O TYR F 57 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N UNK F 64 " --> pdb=" O UNK F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 89 through 102 removed outlier: 3.844A pdb=" N UNK F 94 " --> pdb=" O UNK F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 19 through 32 removed outlier: 3.659A pdb=" N UNK G 29 " --> pdb=" O UNK G 25 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N UNK G 32 " --> pdb=" O UNK G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 54 through 65 removed outlier: 3.857A pdb=" N UNK G 59 " --> pdb=" O UNK G 55 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N UNK G 61 " --> pdb=" O TYR G 57 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N UNK G 64 " --> pdb=" O UNK G 60 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.253A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA C 19 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 34 through 37 Processing sheet with id= C, first strand: chain 'C' and resid 163 through 165 removed outlier: 3.569A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 160 through 162 Processing sheet with id= E, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.519A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.253A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 19 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 34 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 163 through 165 removed outlier: 3.569A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 160 through 162 Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.518A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.253A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 34 through 37 Processing sheet with id= M, first strand: chain 'A' and resid 163 through 165 removed outlier: 3.568A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 160 through 162 Processing sheet with id= O, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.519A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.252A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 19 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 34 through 37 Processing sheet with id= R, first strand: chain 'D' and resid 163 through 165 removed outlier: 3.569A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 160 through 162 Processing sheet with id= T, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.519A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 29 through 31 removed outlier: 4.252A pdb=" N ALA E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA E 19 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 34 through 37 Processing sheet with id= W, first strand: chain 'E' and resid 163 through 165 removed outlier: 3.569A pdb=" N VAL E 163 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 160 through 162 Processing sheet with id= Y, first strand: chain 'E' and resid 238 through 241 removed outlier: 3.519A pdb=" N LYS E 238 " --> pdb=" O ILE E 250 " (cutoff:3.500A) 647 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5116 1.34 - 1.46: 3192 1.46 - 1.57: 7365 1.57 - 1.69: 15 1.69 - 1.81: 185 Bond restraints: 15873 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.78e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.73e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.49e+00 ... (remaining 15868 not shown) Histogram of bond angle deviations from ideal: 96.96 - 104.69: 420 104.69 - 112.42: 8320 112.42 - 120.15: 6432 120.15 - 127.88: 6247 127.88 - 135.61: 160 Bond angle restraints: 21579 Sorted by residual: angle pdb=" C MET B 269 " pdb=" N GLU B 270 " pdb=" CA GLU B 270 " ideal model delta sigma weight residual 123.00 112.84 10.16 1.41e+00 5.03e-01 5.19e+01 angle pdb=" C MET C 269 " pdb=" N GLU C 270 " pdb=" CA GLU C 270 " ideal model delta sigma weight residual 123.00 112.86 10.14 1.41e+00 5.03e-01 5.17e+01 angle pdb=" C MET A 269 " pdb=" N GLU A 270 " pdb=" CA GLU A 270 " ideal model delta sigma weight residual 123.00 112.87 10.13 1.41e+00 5.03e-01 5.16e+01 angle pdb=" C MET D 269 " pdb=" N GLU D 270 " pdb=" CA GLU D 270 " ideal model delta sigma weight residual 123.00 112.88 10.12 1.41e+00 5.03e-01 5.16e+01 angle pdb=" C MET E 269 " pdb=" N GLU E 270 " pdb=" CA GLU E 270 " ideal model delta sigma weight residual 123.00 112.88 10.12 1.41e+00 5.03e-01 5.15e+01 ... (remaining 21574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.09: 8366 19.09 - 38.18: 1015 38.18 - 57.27: 92 57.27 - 76.37: 55 76.37 - 95.46: 5 Dihedral angle restraints: 9533 sinusoidal: 3645 harmonic: 5888 Sorted by residual: dihedral pdb=" CA ILE D 267 " pdb=" C ILE D 267 " pdb=" N GLY D 268 " pdb=" CA GLY D 268 " ideal model delta harmonic sigma weight residual -180.00 -149.87 -30.13 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA ILE C 267 " pdb=" C ILE C 267 " pdb=" N GLY C 268 " pdb=" CA GLY C 268 " ideal model delta harmonic sigma weight residual -180.00 -149.88 -30.12 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA ILE E 267 " pdb=" C ILE E 267 " pdb=" N GLY E 268 " pdb=" CA GLY E 268 " ideal model delta harmonic sigma weight residual -180.00 -149.90 -30.10 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 9530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1321 0.042 - 0.084: 723 0.084 - 0.126: 263 0.126 - 0.168: 76 0.168 - 0.211: 47 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CB THR B 202 " pdb=" CA THR B 202 " pdb=" OG1 THR B 202 " pdb=" CG2 THR B 202 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR D 202 " pdb=" CA THR D 202 " pdb=" OG1 THR D 202 " pdb=" CG2 THR D 202 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2427 not shown) Planarity restraints: 2773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 196 " 0.237 9.50e-02 1.11e+02 1.31e-01 7.95e+01 pdb=" NE ARG B 196 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 196 " 0.145 2.00e-02 2.50e+03 pdb=" NH1 ARG B 196 " -0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG B 196 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 196 " -0.237 9.50e-02 1.11e+02 1.31e-01 7.94e+01 pdb=" NE ARG A 196 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 196 " -0.145 2.00e-02 2.50e+03 pdb=" NH1 ARG A 196 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG A 196 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 196 " -0.237 9.50e-02 1.11e+02 1.31e-01 7.92e+01 pdb=" NE ARG C 196 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 196 " -0.144 2.00e-02 2.50e+03 pdb=" NH1 ARG C 196 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG C 196 " 0.039 2.00e-02 2.50e+03 ... (remaining 2770 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 15 2.19 - 2.86: 6505 2.86 - 3.54: 23284 3.54 - 4.22: 35752 4.22 - 4.90: 57245 Nonbonded interactions: 122801 Sorted by model distance: nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.508 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.546 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.671 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.902 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.939 2.170 ... (remaining 122796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9790 2.51 5 N 2645 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.250 Check model and map are aligned: 0.240 Process input model: 42.710 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 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 : 0.010 0.066 15873 Z= 0.627 Angle : 1.336 10.711 21579 Z= 0.756 Chirality : 0.062 0.211 2430 Planarity : 0.011 0.131 2773 Dihedral : 16.268 95.457 5753 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 1830 helix: -2.08 (0.15), residues: 655 sheet: -0.96 (0.26), residues: 300 loop : -1.82 (0.16), residues: 875 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 847 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 847 average time/residue: 0.2994 time to fit residues: 358.6268 Evaluate side-chains 472 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 1.894 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 371 HIS B 12 ASN B 314 GLN B 360 GLN A 12 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 92 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 296 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 15873 Z= 0.239 Angle : 0.829 10.699 21579 Z= 0.429 Chirality : 0.049 0.190 2430 Planarity : 0.005 0.046 2773 Dihedral : 8.791 59.263 2263 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 1830 helix: -0.68 (0.17), residues: 700 sheet: 0.23 (0.30), residues: 310 loop : -0.77 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 638 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 640 average time/residue: 0.2827 time to fit residues: 267.2753 Evaluate side-chains 449 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 448 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1382 time to fit residues: 2.7043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 360 GLN A 40 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS D 92 ASN D 296 ASN D 360 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 15873 Z= 0.302 Angle : 0.791 9.127 21579 Z= 0.406 Chirality : 0.047 0.181 2430 Planarity : 0.006 0.053 2773 Dihedral : 7.633 43.817 2263 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1830 helix: -0.41 (0.18), residues: 675 sheet: 0.40 (0.30), residues: 295 loop : -0.75 (0.21), residues: 860 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 546 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 547 average time/residue: 0.2656 time to fit residues: 214.8501 Evaluate side-chains 423 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 422 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1387 time to fit residues: 2.7098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.0470 chunk 18 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 chunk 168 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS B 263 GLN B 360 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 92 ASN ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15873 Z= 0.187 Angle : 0.700 12.373 21579 Z= 0.349 Chirality : 0.044 0.169 2430 Planarity : 0.005 0.055 2773 Dihedral : 6.963 48.293 2263 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1830 helix: -0.16 (0.19), residues: 665 sheet: 0.23 (0.29), residues: 300 loop : -0.43 (0.22), residues: 865 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 550 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 551 average time/residue: 0.2584 time to fit residues: 212.7166 Evaluate side-chains 406 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 1.902 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 354 GLN B 360 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 15873 Z= 0.423 Angle : 0.852 8.730 21579 Z= 0.434 Chirality : 0.048 0.182 2430 Planarity : 0.006 0.050 2773 Dihedral : 7.552 58.658 2263 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.84 (0.19), residues: 1830 helix: -0.59 (0.19), residues: 690 sheet: -0.01 (0.29), residues: 295 loop : -0.57 (0.22), residues: 845 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 491 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 493 average time/residue: 0.2597 time to fit residues: 190.5959 Evaluate side-chains 383 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS B 263 GLN B 360 GLN ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 162 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 371 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.7654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 15873 Z= 0.286 Angle : 0.742 7.862 21579 Z= 0.373 Chirality : 0.045 0.254 2430 Planarity : 0.005 0.049 2773 Dihedral : 7.189 58.166 2263 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.85 (0.20), residues: 1830 helix: -0.55 (0.19), residues: 700 sheet: -0.10 (0.30), residues: 295 loop : -0.58 (0.23), residues: 835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.2455 time to fit residues: 180.6766 Evaluate side-chains 382 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 178 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 371 HIS B 263 GLN B 314 GLN B 360 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.8014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15873 Z= 0.188 Angle : 0.702 8.859 21579 Z= 0.349 Chirality : 0.044 0.191 2430 Planarity : 0.005 0.048 2773 Dihedral : 6.670 58.415 2263 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1830 helix: -0.29 (0.19), residues: 670 sheet: -0.26 (0.29), residues: 290 loop : -0.54 (0.22), residues: 870 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 511 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.2469 time to fit residues: 191.5775 Evaluate side-chains 388 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS B 263 GLN B 360 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.8183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 15873 Z= 0.202 Angle : 0.708 10.748 21579 Z= 0.353 Chirality : 0.045 0.402 2430 Planarity : 0.005 0.048 2773 Dihedral : 6.501 59.213 2263 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1830 helix: -0.36 (0.19), residues: 690 sheet: -0.35 (0.29), residues: 290 loop : -0.57 (0.22), residues: 850 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.2541 time to fit residues: 188.4315 Evaluate side-chains 375 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 157 optimal weight: 0.0370 chunk 165 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.3060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 371 HIS B 59 GLN B 121 GLN B 263 GLN B 360 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15873 Z= 0.220 Angle : 0.720 9.023 21579 Z= 0.360 Chirality : 0.046 0.369 2430 Planarity : 0.005 0.050 2773 Dihedral : 6.531 59.994 2263 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1830 helix: -0.38 (0.19), residues: 695 sheet: -0.64 (0.31), residues: 260 loop : -0.58 (0.22), residues: 875 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.2415 time to fit residues: 174.0844 Evaluate side-chains 365 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.928 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS B 121 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 360 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.8500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 15873 Z= 0.291 Angle : 0.769 8.220 21579 Z= 0.391 Chirality : 0.047 0.420 2430 Planarity : 0.005 0.054 2773 Dihedral : 6.866 61.602 2263 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1830 helix: -0.63 (0.18), residues: 725 sheet: -0.65 (0.30), residues: 290 loop : -0.72 (0.22), residues: 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.2344 time to fit residues: 163.1556 Evaluate side-chains 359 residues out of total 1570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 135 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 150 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS B 121 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 360 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113719 restraints weight = 35052.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117132 restraints weight = 21188.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119452 restraints weight = 13952.165| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.8677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15873 Z= 0.188 Angle : 0.706 7.926 21579 Z= 0.355 Chirality : 0.045 0.301 2430 Planarity : 0.005 0.053 2773 Dihedral : 6.492 59.567 2263 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1830 helix: -0.35 (0.20), residues: 670 sheet: -0.52 (0.30), residues: 285 loop : -0.55 (0.22), residues: 875 =============================================================================== Job complete usr+sys time: 3834.96 seconds wall clock time: 69 minutes 50.73 seconds (4190.73 seconds total)