Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:49:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2023/7z7i_14533_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2023/7z7i_14533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2023/7z7i_14533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2023/7z7i_14533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2023/7z7i_14533_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2023/7z7i_14533_updated.pdb" } resolution = 3.5 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 "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "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: 14815 Number of models: 1 Model: "" Number of chains: 10 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: "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: "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: "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: "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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'AR6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'AR6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'AR6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'AR6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ADP': 1, 'AR6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.51, per 1000 atoms: 0.57 Number of scatterers: 14815 At special positions: 0 Unit cell: (101.7, 90, 201.6, 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 20 15.00 Mg 5 11.99 O 2880 8.00 N 2495 7.00 C 9310 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.66 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: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 25 sheets defined 43.1% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.576A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP D 86 " --> pdb=" O MET D 82 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) 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 removed outlier: 3.656A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.136A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 192 " --> pdb=" O TYR D 188 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.706A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 252 through 256 removed outlier: 4.198A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.758A pdb=" N ILE D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.986A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) 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 removed outlier: 3.686A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.608A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.751A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.577A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) 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 removed outlier: 3.657A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.137A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 192 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.706A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 252 through 256 removed outlier: 4.198A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.759A pdb=" N ILE B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.985A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) 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 removed outlier: 3.686A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.608A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.751A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.576A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP E 86 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 91 " --> pdb=" O HIS E 87 " (cutoff:3.500A) 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 removed outlier: 3.656A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.136A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 192 " --> pdb=" O TYR E 188 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.706A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 252 through 256 removed outlier: 4.198A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.758A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.986A pdb=" N TYR E 294 " --> pdb=" O LYS E 291 " (cutoff:3.500A) 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 removed outlier: 3.686A pdb=" N ALA E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 removed outlier: 3.608A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.751A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.576A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP C 86 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) 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 removed outlier: 3.657A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.137A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 192 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.706A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.198A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.757A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.986A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) 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 removed outlier: 3.686A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.608A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.751A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.576A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) 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 removed outlier: 3.656A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.136A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.705A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 252 through 256 removed outlier: 4.198A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.758A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.985A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (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 320 removed outlier: 3.686A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.609A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.751A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 372 Processing sheet with id= A, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.578A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 65 through 69 Processing sheet with id= C, first strand: chain 'D' and resid 103 through 107 removed outlier: 3.508A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.134A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 16 through 19 removed outlier: 3.578A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 65 through 69 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.508A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.134A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'E' and resid 16 through 19 removed outlier: 3.578A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 65 through 69 Processing sheet with id= M, first strand: chain 'E' and resid 103 through 107 removed outlier: 3.508A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.135A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= P, first strand: chain 'C' and resid 16 through 19 removed outlier: 3.579A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= R, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.507A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.134A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'A' and resid 16 through 19 removed outlier: 3.578A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 65 through 69 Processing sheet with id= W, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.508A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.134A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 238 through 241 450 hydrogen bonds defined for protein. 1065 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: 4.31 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4785 1.34 - 1.46: 2649 1.46 - 1.57: 7476 1.57 - 1.69: 35 1.69 - 1.81: 205 Bond restraints: 15150 Sorted by residual: bond pdb=" C1' AR6 E 403 " pdb=" O4' AR6 E 403 " ideal model delta sigma weight residual 1.396 1.647 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C1' AR6 A 403 " pdb=" O4' AR6 A 403 " ideal model delta sigma weight residual 1.396 1.647 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C1' AR6 B 403 " pdb=" O4' AR6 B 403 " ideal model delta sigma weight residual 1.396 1.647 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C1' AR6 D 403 " pdb=" O4' AR6 D 403 " ideal model delta sigma weight residual 1.396 1.647 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C1' AR6 C 403 " pdb=" O4' AR6 C 403 " ideal model delta sigma weight residual 1.396 1.646 -0.250 2.00e-02 2.50e+03 1.57e+02 ... (remaining 15145 not shown) Histogram of bond angle deviations from ideal: 97.11 - 105.36: 445 105.36 - 113.62: 8550 113.62 - 121.88: 8715 121.88 - 130.14: 2784 130.14 - 138.40: 101 Bond angle restraints: 20595 Sorted by residual: angle pdb=" C1' AR6 D 403 " pdb=" O4' AR6 D 403 " pdb=" C4' AR6 D 403 " ideal model delta sigma weight residual 110.85 97.11 13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C1' AR6 A 403 " pdb=" O4' AR6 A 403 " pdb=" C4' AR6 A 403 " ideal model delta sigma weight residual 110.85 97.11 13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C1' AR6 E 403 " pdb=" O4' AR6 E 403 " pdb=" C4' AR6 E 403 " ideal model delta sigma weight residual 110.85 97.11 13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C1' AR6 C 403 " pdb=" O4' AR6 C 403 " pdb=" C4' AR6 C 403 " ideal model delta sigma weight residual 110.85 97.11 13.74 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C1' AR6 B 403 " pdb=" O4' AR6 B 403 " pdb=" C4' AR6 B 403 " ideal model delta sigma weight residual 110.85 97.16 13.69 3.00e+00 1.11e-01 2.08e+01 ... (remaining 20590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 8446 18.64 - 37.28: 409 37.28 - 55.92: 75 55.92 - 74.55: 45 74.55 - 93.19: 40 Dihedral angle restraints: 9015 sinusoidal: 3655 harmonic: 5360 Sorted by residual: dihedral pdb=" CA LEU E 65 " pdb=" C LEU E 65 " pdb=" N THR E 66 " pdb=" CA THR E 66 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N THR A 66 " pdb=" CA THR A 66 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LEU B 65 " pdb=" C LEU B 65 " pdb=" N THR B 66 " pdb=" CA THR B 66 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 9012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2162 0.121 - 0.242: 103 0.242 - 0.364: 5 0.364 - 0.485: 11 0.485 - 0.606: 9 Chirality restraints: 2290 Sorted by residual: chirality pdb=" C4D AR6 C 403 " pdb=" C3D AR6 C 403 " pdb=" C5D AR6 C 403 " pdb=" O4D AR6 C 403 " both_signs ideal model delta sigma weight residual False -2.53 -3.13 0.61 2.00e-01 2.50e+01 9.18e+00 chirality pdb=" C4D AR6 B 403 " pdb=" C3D AR6 B 403 " pdb=" C5D AR6 B 403 " pdb=" O4D AR6 B 403 " both_signs ideal model delta sigma weight residual False -2.53 -3.13 0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C4D AR6 D 403 " pdb=" C3D AR6 D 403 " pdb=" C5D AR6 D 403 " pdb=" O4D AR6 D 403 " both_signs ideal model delta sigma weight residual False -2.53 -3.13 0.60 2.00e-01 2.50e+01 9.07e+00 ... (remaining 2287 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 62 " -0.065 9.50e-02 1.11e+02 3.98e-02 9.59e+00 pdb=" NE ARG C 62 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 62 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG C 62 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 62 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 62 " 0.066 9.50e-02 1.11e+02 3.99e-02 9.51e+00 pdb=" NE ARG B 62 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 62 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 62 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B 62 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 62 " -0.065 9.50e-02 1.11e+02 3.95e-02 9.50e+00 pdb=" NE ARG A 62 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 62 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 62 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 62 " 0.015 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 81 2.54 - 3.13: 11815 3.13 - 3.72: 19998 3.72 - 4.31: 29527 4.31 - 4.90: 47426 Nonbonded interactions: 108847 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.952 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 1.953 2.170 ... (remaining 108842 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 20 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9310 2.51 5 N 2495 2.21 5 O 2880 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.440 Check model and map are aligned: 0.240 Process input model: 39.860 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.014 0.251 15150 Z= 0.918 Angle : 1.068 13.744 20595 Z= 0.527 Chirality : 0.073 0.606 2290 Planarity : 0.005 0.040 2600 Dihedral : 14.693 93.192 5585 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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: -2.47 (0.18), residues: 1830 helix: -2.68 (0.14), residues: 650 sheet: -0.24 (0.29), residues: 315 loop : -1.18 (0.20), residues: 865 *********************** 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 189 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.850 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2650 time to fit residues: 74.8480 Evaluate side-chains 108 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2063 ------------------------------------------------------------------------------- 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: 1.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN D 162 ASN B 115 ASN B 128 ASN E 115 ASN E 162 ASN C 115 ASN C 128 ASN C 162 ASN A 115 ASN A 162 ASN A 371 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15150 Z= 0.272 Angle : 0.668 6.540 20595 Z= 0.329 Chirality : 0.046 0.143 2290 Planarity : 0.004 0.042 2600 Dihedral : 9.060 84.184 2105 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1830 helix: -1.03 (0.19), residues: 655 sheet: -0.73 (0.29), residues: 305 loop : -0.45 (0.20), residues: 870 *********************** 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 151 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 137 average time/residue: 0.2310 time to fit residues: 50.1136 Evaluate side-chains 115 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1297 time to fit residues: 5.5078 ------------------------------------------------------------------------------- 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: 10.0000 chunk 52 optimal weight: 0.0570 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 ASN E 161 HIS A 12 ASN A 115 ASN A 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 15150 Z= 0.346 Angle : 0.666 6.397 20595 Z= 0.326 Chirality : 0.046 0.160 2290 Planarity : 0.004 0.045 2600 Dihedral : 8.838 85.167 2105 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 1.47 % 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: -0.74 (0.20), residues: 1830 helix: -0.39 (0.21), residues: 605 sheet: -0.84 (0.29), residues: 340 loop : -0.24 (0.21), residues: 885 *********************** 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 128 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.762 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 119 average time/residue: 0.2161 time to fit residues: 42.3198 Evaluate side-chains 110 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1348 time to fit residues: 5.5398 ------------------------------------------------------------------------------- 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: 6.9990 chunk 126 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 113 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN E 371 HIS C 115 ASN C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15150 Z= 0.121 Angle : 0.534 6.201 20595 Z= 0.249 Chirality : 0.041 0.126 2290 Planarity : 0.004 0.038 2600 Dihedral : 7.990 82.670 2105 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.77 % 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: -0.17 (0.20), residues: 1830 helix: 0.13 (0.21), residues: 645 sheet: -0.37 (0.28), residues: 330 loop : 0.00 (0.22), residues: 855 *********************** 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 125 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 120 average time/residue: 0.2349 time to fit residues: 45.4762 Evaluate side-chains 105 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1292 time to fit residues: 3.5218 ------------------------------------------------------------------------------- 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: 10.0000 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 160 optimal weight: 0.0980 chunk 45 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 15150 Z= 0.136 Angle : 0.530 7.457 20595 Z= 0.244 Chirality : 0.042 0.126 2290 Planarity : 0.003 0.042 2600 Dihedral : 7.737 80.080 2105 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.83 % 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: 0.10 (0.20), residues: 1830 helix: 0.39 (0.22), residues: 645 sheet: -0.25 (0.28), residues: 325 loop : 0.12 (0.22), residues: 860 *********************** 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 114 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.812 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 108 average time/residue: 0.2283 time to fit residues: 40.3750 Evaluate side-chains 106 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1362 time to fit residues: 4.4863 ------------------------------------------------------------------------------- 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: 10.0000 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.057 15150 Z= 0.563 Angle : 0.786 8.181 20595 Z= 0.385 Chirality : 0.051 0.194 2290 Planarity : 0.005 0.054 2600 Dihedral : 8.914 92.716 2105 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 1.21 % 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: -0.85 (0.20), residues: 1830 helix: -0.29 (0.21), residues: 625 sheet: -1.15 (0.27), residues: 345 loop : -0.33 (0.22), residues: 860 *********************** 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 112 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.2200 time to fit residues: 38.7109 Evaluate side-chains 103 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.806 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1261 time to fit residues: 5.0280 ------------------------------------------------------------------------------- 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: 2.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 0.4980 chunk 82 optimal weight: 0.4980 chunk 110 optimal weight: 0.0050 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN E 115 ASN E 280 ASN C 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 15150 Z= 0.126 Angle : 0.551 9.719 20595 Z= 0.253 Chirality : 0.042 0.126 2290 Planarity : 0.004 0.043 2600 Dihedral : 7.969 82.487 2105 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.45 % 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: -0.17 (0.20), residues: 1830 helix: 0.35 (0.22), residues: 635 sheet: -0.46 (0.28), residues: 315 loop : -0.18 (0.22), residues: 880 *********************** 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 107 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.872 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 0.2394 time to fit residues: 40.6894 Evaluate side-chains 98 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1571 time to fit residues: 3.3872 ------------------------------------------------------------------------------- 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: 0.9980 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 15150 Z= 0.164 Angle : 0.547 9.190 20595 Z= 0.251 Chirality : 0.042 0.128 2290 Planarity : 0.004 0.044 2600 Dihedral : 7.761 82.187 2105 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.32 % 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: -0.01 (0.20), residues: 1830 helix: 0.50 (0.22), residues: 635 sheet: -0.38 (0.28), residues: 315 loop : -0.08 (0.22), residues: 880 *********************** 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 105 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 2.083 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 102 average time/residue: 0.2281 time to fit residues: 38.1236 Evaluate side-chains 100 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.829 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1321 time to fit residues: 3.4532 ------------------------------------------------------------------------------- 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: 10.0000 chunk 155 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15150 Z= 0.229 Angle : 0.584 11.737 20595 Z= 0.270 Chirality : 0.043 0.174 2290 Planarity : 0.004 0.044 2600 Dihedral : 7.815 82.818 2105 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.09 (0.20), residues: 1830 helix: 0.50 (0.22), residues: 635 sheet: -0.46 (0.27), residues: 335 loop : -0.17 (0.22), residues: 860 *********************** 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 100 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.688 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 98 average time/residue: 0.2469 time to fit residues: 39.0646 Evaluate side-chains 95 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1694 time to fit residues: 2.7716 ------------------------------------------------------------------------------- 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: 0.8980 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 116 optimal weight: 0.0270 overall best weight: 2.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 15150 Z= 0.205 Angle : 0.584 11.308 20595 Z= 0.266 Chirality : 0.043 0.158 2290 Planarity : 0.004 0.045 2600 Dihedral : 7.726 83.236 2105 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.05 (0.20), residues: 1830 helix: 0.56 (0.22), residues: 635 sheet: -0.36 (0.28), residues: 315 loop : -0.21 (0.22), residues: 880 ********************** 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 98 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.659 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 97 average time/residue: 0.2353 time to fit residues: 37.5998 Evaluate side-chains 95 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5814 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.065271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053087 restraints weight = 52260.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.055186 restraints weight = 28191.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056633 restraints weight = 18613.845| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 15150 Z= 0.201 Angle : 0.576 11.332 20595 Z= 0.264 Chirality : 0.043 0.176 2290 Planarity : 0.004 0.044 2600 Dihedral : 7.641 83.622 2105 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.02 (0.20), residues: 1830 helix: 0.60 (0.22), residues: 635 sheet: -0.37 (0.28), residues: 315 loop : -0.21 (0.22), residues: 880 =============================================================================== Job complete usr+sys time: 2118.85 seconds wall clock time: 40 minutes 4.20 seconds (2404.20 seconds total)