Starting phenix.real_space_refine on Fri Feb 16 08:44:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2024/7z7i_14533_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2024/7z7i_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_2024/7z7i_14533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2024/7z7i_14533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2024/7z7i_14533_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7i_14533/02_2024/7z7i_14533_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. 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-5238/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, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 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, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 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, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 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, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 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, 'APR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.33, per 1000 atoms: 0.56 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: 5.81 Conformation dependent library (CDL) restraints added in 3.0 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: 3.20 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: 4.21 Time building geometry restraints manager: 6.24 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' APR E 403 " pdb=" O4' APR E 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR A 403 " pdb=" O4' APR A 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR B 403 " pdb=" O4' APR B 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR D 403 " pdb=" O4' APR D 403 " ideal model delta sigma weight residual 1.393 1.647 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C1' APR C 403 " pdb=" O4' APR C 403 " ideal model delta sigma weight residual 1.393 1.646 -0.253 2.00e-02 2.50e+03 1.60e+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' APR D 403 " pdb=" O4' APR D 403 " pdb=" C4' APR D 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR A 403 " pdb=" O4' APR A 403 " pdb=" C4' APR A 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR E 403 " pdb=" O4' APR E 403 " pdb=" C4' APR E 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR C 403 " pdb=" O4' APR C 403 " pdb=" C4' APR C 403 " ideal model delta sigma weight residual 111.27 97.11 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C1' APR B 403 " pdb=" O4' APR B 403 " pdb=" C4' APR B 403 " ideal model delta sigma weight residual 111.27 97.16 14.11 3.00e+00 1.11e-01 2.21e+01 ... (remaining 20590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 8586 18.64 - 37.28: 477 37.28 - 55.92: 82 55.92 - 74.55: 50 74.55 - 93.19: 30 Dihedral angle restraints: 9225 sinusoidal: 3865 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 9222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2191 0.129 - 0.258: 74 0.258 - 0.387: 5 0.387 - 0.516: 15 0.516 - 0.645: 5 Chirality restraints: 2290 Sorted by residual: chirality pdb=" C4D APR C 403 " pdb=" C3D APR C 403 " pdb=" C5D APR C 403 " pdb=" O4D APR C 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C4D APR B 403 " pdb=" C3D APR B 403 " pdb=" C5D APR B 403 " pdb=" O4D APR B 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C4D APR D 403 " pdb=" C3D APR D 403 " pdb=" C5D APR D 403 " pdb=" O4D APR D 403 " both_signs ideal model delta sigma weight residual False -2.49 -3.13 0.64 2.00e-01 2.50e+01 1.03e+01 ... (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 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: 1.530 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: 7.440 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 41.950 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 0.254 15150 Z= 0.919 Angle : 1.078 14.164 20595 Z= 0.529 Chirality : 0.073 0.645 2290 Planarity : 0.005 0.040 2600 Dihedral : 14.644 93.192 5795 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 % Allowed : 2.56 % Favored : 97.44 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 86 HIS 0.004 0.001 HIS C 88 PHE 0.015 0.002 PHE A 255 TYR 0.014 0.005 TYR A 143 ARG 0.052 0.008 ARG C 62 *********************** 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 : 1.870 Fit side-chains revert: symmetry clash REVERT: D 286 ASP cc_start: 0.8559 (m-30) cc_final: 0.8276 (m-30) REVERT: D 355 MET cc_start: 0.8814 (mmm) cc_final: 0.8516 (mmm) REVERT: B 176 MET cc_start: 0.8100 (mmt) cc_final: 0.7685 (mmp) REVERT: B 355 MET cc_start: 0.8936 (mmm) cc_final: 0.8612 (mmm) REVERT: E 82 MET cc_start: 0.8690 (tpt) cc_final: 0.8392 (tpp) REVERT: E 355 MET cc_start: 0.7804 (mmm) cc_final: 0.6877 (mpp) REVERT: C 137 GLN cc_start: 0.8914 (mt0) cc_final: 0.8432 (mt0) REVERT: C 355 MET cc_start: 0.8695 (mmm) cc_final: 0.8265 (mpp) REVERT: A 82 MET cc_start: 0.9025 (tpt) cc_final: 0.8692 (tpt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2682 time to fit residues: 76.2582 Evaluate side-chains 109 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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: 3.9990 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: 9.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15150 Z= 0.302 Angle : 0.675 6.787 20595 Z= 0.334 Chirality : 0.046 0.148 2290 Planarity : 0.004 0.043 2600 Dihedral : 8.914 78.401 2315 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.66 % Allowed : 6.39 % Favored : 91.95 % 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: -1.24 (0.19), residues: 1830 helix: -1.05 (0.19), residues: 645 sheet: -0.38 (0.30), residues: 280 loop : -0.65 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.004 0.001 HIS E 101 PHE 0.016 0.002 PHE A 124 TYR 0.011 0.002 TYR B 240 ARG 0.005 0.001 ARG B 28 *********************** 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 148 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 162 ASN cc_start: 0.8404 (m-40) cc_final: 0.8128 (m-40) REVERT: D 269 MET cc_start: 0.7816 (tpp) cc_final: 0.6889 (ttp) REVERT: D 286 ASP cc_start: 0.8552 (m-30) cc_final: 0.8350 (m-30) REVERT: D 355 MET cc_start: 0.8944 (mmm) cc_final: 0.8608 (mmm) REVERT: B 123 MET cc_start: 0.8591 (tpp) cc_final: 0.8361 (tpp) REVERT: B 176 MET cc_start: 0.7517 (mmt) cc_final: 0.7185 (mmt) REVERT: B 227 MET cc_start: 0.8317 (ttm) cc_final: 0.8092 (tpp) REVERT: B 355 MET cc_start: 0.9000 (mmm) cc_final: 0.8658 (mmm) REVERT: E 190 MET cc_start: 0.7442 (mmm) cc_final: 0.7241 (mmt) REVERT: E 355 MET cc_start: 0.7997 (mmm) cc_final: 0.6937 (mtm) REVERT: C 187 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: C 355 MET cc_start: 0.8772 (mmm) cc_final: 0.8382 (mpp) REVERT: A 82 MET cc_start: 0.8853 (tpt) cc_final: 0.8520 (tpt) REVERT: A 269 MET cc_start: 0.7481 (mmp) cc_final: 0.6727 (tpp) outliers start: 26 outliers final: 14 residues processed: 136 average time/residue: 0.2339 time to fit residues: 50.5029 Evaluate side-chains 119 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 117 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 0.0270 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 0.0970 overall best weight: 3.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 ASN A 115 ASN A 128 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15150 Z= 0.269 Angle : 0.618 6.297 20595 Z= 0.298 Chirality : 0.045 0.148 2290 Planarity : 0.004 0.043 2600 Dihedral : 8.082 79.497 2315 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.04 % Allowed : 7.35 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1830 helix: -0.40 (0.20), residues: 635 sheet: -0.78 (0.29), residues: 305 loop : -0.24 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.003 0.001 HIS E 101 PHE 0.013 0.001 PHE C 124 TYR 0.013 0.001 TYR C 143 ARG 0.003 0.000 ARG B 28 *********************** 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 143 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 47 MET cc_start: 0.8174 (ptm) cc_final: 0.7973 (ppp) REVERT: D 269 MET cc_start: 0.8044 (tpp) cc_final: 0.7320 (mtt) REVERT: D 355 MET cc_start: 0.9023 (mmm) cc_final: 0.8673 (mmm) REVERT: B 176 MET cc_start: 0.7569 (mmt) cc_final: 0.7150 (mpp) REVERT: B 227 MET cc_start: 0.8265 (ttm) cc_final: 0.7963 (tpp) REVERT: B 355 MET cc_start: 0.9044 (mmm) cc_final: 0.8629 (mmm) REVERT: E 47 MET cc_start: 0.6997 (pmm) cc_final: 0.5706 (ttt) REVERT: E 190 MET cc_start: 0.7618 (mmm) cc_final: 0.7307 (mmm) REVERT: E 355 MET cc_start: 0.8241 (mmm) cc_final: 0.7409 (mtm) REVERT: C 44 MET cc_start: 0.8484 (mmm) cc_final: 0.8136 (mmm) REVERT: C 187 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: C 355 MET cc_start: 0.8779 (mmm) cc_final: 0.8552 (mmm) REVERT: A 82 MET cc_start: 0.8849 (tpt) cc_final: 0.8248 (tpp) REVERT: A 269 MET cc_start: 0.8234 (mmp) cc_final: 0.7553 (tpp) outliers start: 32 outliers final: 23 residues processed: 132 average time/residue: 0.2258 time to fit residues: 47.8858 Evaluate side-chains 121 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 356 TRP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain A residue 162 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 280 ASN A 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15150 Z= 0.337 Angle : 0.641 6.353 20595 Z= 0.309 Chirality : 0.046 0.158 2290 Planarity : 0.004 0.043 2600 Dihedral : 7.953 85.484 2315 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.30 % Allowed : 8.63 % Favored : 89.07 % 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: -0.68 (0.20), residues: 1830 helix: -0.19 (0.21), residues: 630 sheet: -1.01 (0.28), residues: 340 loop : -0.23 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS C 88 PHE 0.013 0.001 PHE C 21 TYR 0.013 0.001 TYR B 240 ARG 0.002 0.000 ARG D 177 *********************** 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 134 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.8195 (ptm) cc_final: 0.7506 (ppp) REVERT: D 269 MET cc_start: 0.8181 (tpp) cc_final: 0.7479 (mtt) REVERT: D 355 MET cc_start: 0.8979 (mmm) cc_final: 0.8609 (mmm) REVERT: B 176 MET cc_start: 0.7617 (mmt) cc_final: 0.7138 (mpp) REVERT: B 227 MET cc_start: 0.8282 (ttm) cc_final: 0.7788 (tpp) REVERT: B 355 MET cc_start: 0.9034 (mmm) cc_final: 0.8728 (mmm) REVERT: E 44 MET cc_start: 0.5913 (tpt) cc_final: 0.5538 (tpt) REVERT: E 47 MET cc_start: 0.6882 (pmm) cc_final: 0.5846 (ttt) REVERT: E 190 MET cc_start: 0.7569 (mmm) cc_final: 0.7290 (mmm) REVERT: E 269 MET cc_start: 0.7301 (mmm) cc_final: 0.6839 (mtt) REVERT: E 355 MET cc_start: 0.8291 (mmm) cc_final: 0.7470 (mtm) REVERT: C 44 MET cc_start: 0.8625 (mmm) cc_final: 0.8070 (mmm) REVERT: C 47 MET cc_start: 0.7608 (mtp) cc_final: 0.7299 (mtp) REVERT: C 187 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: C 269 MET cc_start: 0.8079 (tpp) cc_final: 0.7656 (mmp) REVERT: C 355 MET cc_start: 0.8787 (mmm) cc_final: 0.8586 (mmm) REVERT: A 44 MET cc_start: 0.8908 (tpt) cc_final: 0.8643 (tpp) REVERT: A 82 MET cc_start: 0.8946 (tpt) cc_final: 0.8357 (tpp) REVERT: A 161 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7923 (p90) outliers start: 36 outliers final: 29 residues processed: 128 average time/residue: 0.2151 time to fit residues: 45.1398 Evaluate side-chains 127 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 96 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 356 TRP Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 257 CYS 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: 3.9990 chunk 133 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15150 Z= 0.150 Angle : 0.539 8.395 20595 Z= 0.250 Chirality : 0.042 0.127 2290 Planarity : 0.004 0.044 2600 Dihedral : 7.334 76.936 2315 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.85 % Allowed : 9.14 % Favored : 89.01 % 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: -0.21 (0.20), residues: 1830 helix: 0.29 (0.22), residues: 635 sheet: -0.56 (0.27), residues: 335 loop : -0.12 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 79 HIS 0.002 0.000 HIS E 371 PHE 0.007 0.001 PHE A 223 TYR 0.009 0.001 TYR E 218 ARG 0.002 0.000 ARG B 256 *********************** 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 130 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 2.418 Fit side-chains revert: symmetry clash REVERT: D 47 MET cc_start: 0.8055 (ptm) cc_final: 0.7429 (ppp) REVERT: D 227 MET cc_start: 0.8962 (ttm) cc_final: 0.8620 (ttm) REVERT: D 269 MET cc_start: 0.8077 (tpp) cc_final: 0.7358 (mtt) REVERT: D 355 MET cc_start: 0.8929 (mmm) cc_final: 0.8562 (mmm) REVERT: B 187 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8230 (m-30) REVERT: B 227 MET cc_start: 0.8197 (ttm) cc_final: 0.7839 (tpp) REVERT: B 355 MET cc_start: 0.8996 (mmm) cc_final: 0.8749 (mmm) REVERT: E 47 MET cc_start: 0.6890 (pmm) cc_final: 0.5921 (ttt) REVERT: E 190 MET cc_start: 0.7475 (mmm) cc_final: 0.7203 (mmm) REVERT: E 269 MET cc_start: 0.7109 (mmm) cc_final: 0.6598 (mtt) REVERT: E 355 MET cc_start: 0.8078 (mmm) cc_final: 0.7535 (mtm) REVERT: C 47 MET cc_start: 0.7614 (mtp) cc_final: 0.7271 (mtp) REVERT: C 187 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: C 355 MET cc_start: 0.8651 (mmm) cc_final: 0.8408 (mmm) REVERT: A 44 MET cc_start: 0.8900 (tpt) cc_final: 0.8672 (tpp) REVERT: A 82 MET cc_start: 0.8816 (tpt) cc_final: 0.8181 (tpp) REVERT: A 161 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7832 (p90) outliers start: 29 outliers final: 20 residues processed: 125 average time/residue: 0.2627 time to fit residues: 53.4500 Evaluate side-chains 120 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 162 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 ASN C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15150 Z= 0.451 Angle : 0.702 7.037 20595 Z= 0.339 Chirality : 0.048 0.173 2290 Planarity : 0.005 0.049 2600 Dihedral : 7.889 90.813 2315 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.49 % Allowed : 9.52 % Favored : 87.99 % 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: -0.82 (0.20), residues: 1830 helix: -0.14 (0.21), residues: 630 sheet: -1.15 (0.27), residues: 340 loop : -0.42 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 79 HIS 0.006 0.001 HIS C 88 PHE 0.015 0.002 PHE C 21 TYR 0.012 0.002 TYR B 240 ARG 0.003 0.000 ARG C 177 *********************** 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 134 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 95 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 47 MET cc_start: 0.8188 (ptm) cc_final: 0.7615 (ppp) REVERT: D 269 MET cc_start: 0.8289 (tpp) cc_final: 0.7607 (mtt) REVERT: D 355 MET cc_start: 0.8929 (mmm) cc_final: 0.8606 (mmm) REVERT: B 44 MET cc_start: 0.8518 (ttp) cc_final: 0.7462 (tmm) REVERT: B 187 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: B 313 MET cc_start: 0.8555 (tpp) cc_final: 0.8349 (ttm) REVERT: B 355 MET cc_start: 0.9039 (mmm) cc_final: 0.8703 (mmm) REVERT: E 47 MET cc_start: 0.6951 (pmm) cc_final: 0.6101 (ttt) REVERT: E 269 MET cc_start: 0.7530 (mmm) cc_final: 0.7173 (mtt) REVERT: E 355 MET cc_start: 0.8088 (mmm) cc_final: 0.7530 (mtm) REVERT: C 44 MET cc_start: 0.8612 (mmm) cc_final: 0.7841 (mmm) REVERT: C 47 MET cc_start: 0.7715 (mtp) cc_final: 0.7343 (mtp) REVERT: C 187 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: C 269 MET cc_start: 0.8268 (tpp) cc_final: 0.7807 (mmp) REVERT: C 355 MET cc_start: 0.8731 (mmm) cc_final: 0.8525 (mmm) REVERT: A 44 MET cc_start: 0.8926 (tpt) cc_final: 0.8674 (tpp) REVERT: A 82 MET cc_start: 0.8976 (tpt) cc_final: 0.8352 (tpp) REVERT: A 269 MET cc_start: 0.8509 (mmp) cc_final: 0.8279 (mmp) outliers start: 39 outliers final: 31 residues processed: 128 average time/residue: 0.2094 time to fit residues: 44.2509 Evaluate side-chains 126 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain C residue 10 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 260 THR 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: 0.5980 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15150 Z= 0.122 Angle : 0.531 8.058 20595 Z= 0.245 Chirality : 0.042 0.127 2290 Planarity : 0.004 0.044 2600 Dihedral : 7.058 78.343 2315 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.92 % Allowed : 10.16 % Favored : 87.92 % 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: -0.19 (0.20), residues: 1830 helix: 0.33 (0.22), residues: 640 sheet: -0.46 (0.29), residues: 305 loop : -0.20 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.004 0.000 HIS B 88 PHE 0.010 0.001 PHE A 223 TYR 0.009 0.001 TYR E 218 ARG 0.002 0.000 ARG B 256 *********************** 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 132 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 2.006 Fit side-chains revert: symmetry clash REVERT: D 227 MET cc_start: 0.8954 (ttm) cc_final: 0.8729 (ttm) REVERT: D 269 MET cc_start: 0.8142 (tpp) cc_final: 0.7379 (mtt) REVERT: D 355 MET cc_start: 0.8877 (mmm) cc_final: 0.8517 (mmm) REVERT: B 44 MET cc_start: 0.8436 (ttp) cc_final: 0.7442 (tmm) REVERT: B 187 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: B 227 MET cc_start: 0.8292 (tpp) cc_final: 0.7837 (tpp) REVERT: B 313 MET cc_start: 0.8538 (tpp) cc_final: 0.8111 (ttm) REVERT: B 355 MET cc_start: 0.8996 (mmm) cc_final: 0.8734 (mmm) REVERT: E 47 MET cc_start: 0.7007 (pmm) cc_final: 0.6086 (ttt) REVERT: E 269 MET cc_start: 0.7142 (mmm) cc_final: 0.6656 (mtt) REVERT: E 355 MET cc_start: 0.8009 (mmm) cc_final: 0.7633 (mtm) REVERT: C 47 MET cc_start: 0.7759 (mtp) cc_final: 0.7368 (mtp) REVERT: A 44 MET cc_start: 0.8926 (tpt) cc_final: 0.8660 (tpp) REVERT: A 82 MET cc_start: 0.8731 (tpt) cc_final: 0.8460 (tpt) REVERT: A 124 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: A 161 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7852 (p90) REVERT: A 269 MET cc_start: 0.8401 (mmp) cc_final: 0.8085 (mmp) outliers start: 30 outliers final: 24 residues processed: 123 average time/residue: 0.2396 time to fit residues: 47.8501 Evaluate side-chains 127 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 257 CYS 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: 9.9990 chunk 53 optimal weight: 0.0000 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 0.0030 chunk 121 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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: 0.8019 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15150 Z= 0.125 Angle : 0.519 8.778 20595 Z= 0.237 Chirality : 0.041 0.125 2290 Planarity : 0.004 0.044 2600 Dihedral : 6.679 70.836 2315 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.47 % Allowed : 10.54 % Favored : 87.99 % 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: -0.03 (0.20), residues: 1830 helix: 0.32 (0.22), residues: 670 sheet: -0.34 (0.28), residues: 305 loop : 0.01 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.003 0.000 HIS B 88 PHE 0.010 0.001 PHE A 223 TYR 0.009 0.001 TYR E 218 ARG 0.003 0.000 ARG E 312 *********************** 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 128 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.810 Fit side-chains revert: symmetry clash REVERT: D 187 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: D 355 MET cc_start: 0.8865 (mmm) cc_final: 0.8490 (mmm) REVERT: B 44 MET cc_start: 0.8452 (ttp) cc_final: 0.7461 (tmm) REVERT: B 187 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: B 227 MET cc_start: 0.8369 (tpp) cc_final: 0.7902 (tpp) REVERT: B 313 MET cc_start: 0.8485 (tpp) cc_final: 0.8110 (ttm) REVERT: B 355 MET cc_start: 0.8860 (mmm) cc_final: 0.8583 (mmm) REVERT: E 47 MET cc_start: 0.6990 (pmm) cc_final: 0.6183 (ttt) REVERT: E 355 MET cc_start: 0.7993 (mmm) cc_final: 0.7690 (mtm) REVERT: C 47 MET cc_start: 0.7618 (mtp) cc_final: 0.7278 (mtp) REVERT: C 283 MET cc_start: 0.8337 (mmp) cc_final: 0.8007 (mmp) REVERT: A 44 MET cc_start: 0.8931 (tpt) cc_final: 0.8677 (tpp) REVERT: A 82 MET cc_start: 0.8775 (tpt) cc_final: 0.8498 (tpt) REVERT: A 176 MET cc_start: 0.8400 (tpp) cc_final: 0.7961 (tpp) REVERT: A 269 MET cc_start: 0.8176 (mmp) cc_final: 0.7794 (mmp) outliers start: 23 outliers final: 20 residues processed: 121 average time/residue: 0.2168 time to fit residues: 42.7950 Evaluate side-chains 120 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 162 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15150 Z= 0.347 Angle : 0.641 10.299 20595 Z= 0.304 Chirality : 0.046 0.160 2290 Planarity : 0.004 0.047 2600 Dihedral : 7.197 82.461 2315 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.11 % Allowed : 10.10 % Favored : 87.80 % 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: -0.27 (0.20), residues: 1830 helix: 0.37 (0.22), residues: 625 sheet: -0.62 (0.27), residues: 335 loop : -0.25 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 79 HIS 0.004 0.001 HIS C 88 PHE 0.013 0.001 PHE C 21 TYR 0.011 0.001 TYR B 240 ARG 0.003 0.000 ARG D 177 *********************** 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 131 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 269 MET cc_start: 0.7893 (mmp) cc_final: 0.7517 (mtm) REVERT: B 44 MET cc_start: 0.8465 (ttp) cc_final: 0.7404 (tmm) REVERT: B 187 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: B 227 MET cc_start: 0.8308 (tpp) cc_final: 0.7795 (tpp) REVERT: B 313 MET cc_start: 0.8531 (tpp) cc_final: 0.8276 (ttm) REVERT: B 355 MET cc_start: 0.9016 (mmm) cc_final: 0.8725 (mmm) REVERT: E 47 MET cc_start: 0.6983 (pmm) cc_final: 0.6263 (ttt) REVERT: E 269 MET cc_start: 0.7370 (mmm) cc_final: 0.6962 (mtt) REVERT: E 286 ASP cc_start: 0.8088 (p0) cc_final: 0.7785 (p0) REVERT: E 355 MET cc_start: 0.8062 (mmm) cc_final: 0.7606 (mtm) REVERT: C 47 MET cc_start: 0.7711 (mtp) cc_final: 0.7373 (mtp) REVERT: C 227 MET cc_start: 0.8646 (mmm) cc_final: 0.8163 (tpp) REVERT: A 44 MET cc_start: 0.8938 (tpt) cc_final: 0.8719 (tpp) REVERT: A 82 MET cc_start: 0.8935 (tpt) cc_final: 0.8360 (tpp) REVERT: A 161 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7851 (p90) outliers start: 33 outliers final: 27 residues processed: 124 average time/residue: 0.2394 time to fit residues: 48.1963 Evaluate side-chains 124 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15150 Z= 0.173 Angle : 0.569 10.376 20595 Z= 0.260 Chirality : 0.042 0.132 2290 Planarity : 0.004 0.045 2600 Dihedral : 6.825 75.135 2315 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.92 % Allowed : 10.73 % Favored : 87.35 % 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: -0.16 (0.20), residues: 1830 helix: 0.52 (0.22), residues: 635 sheet: -0.56 (0.27), residues: 335 loop : -0.25 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 79 HIS 0.003 0.000 HIS B 88 PHE 0.010 0.001 PHE A 223 TYR 0.009 0.001 TYR E 218 ARG 0.002 0.000 ARG A 177 ********************** 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 127 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 2.140 Fit side-chains revert: symmetry clash REVERT: D 132 MET cc_start: 0.8657 (tmm) cc_final: 0.8421 (tmm) REVERT: D 269 MET cc_start: 0.7892 (mmp) cc_final: 0.7471 (mtm) REVERT: B 44 MET cc_start: 0.8414 (ttp) cc_final: 0.7369 (tmm) REVERT: B 187 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: B 227 MET cc_start: 0.8300 (tpp) cc_final: 0.7806 (tpp) REVERT: B 313 MET cc_start: 0.8525 (tpp) cc_final: 0.8165 (ttm) REVERT: B 355 MET cc_start: 0.8947 (mmm) cc_final: 0.8659 (mmm) REVERT: E 47 MET cc_start: 0.6878 (pmm) cc_final: 0.6209 (ttt) REVERT: E 269 MET cc_start: 0.7216 (mmm) cc_final: 0.6734 (mtt) REVERT: E 284 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8368 (mtmt) REVERT: E 286 ASP cc_start: 0.8041 (p0) cc_final: 0.7749 (p0) REVERT: E 355 MET cc_start: 0.7986 (mmm) cc_final: 0.7638 (mtm) REVERT: C 47 MET cc_start: 0.7662 (mtp) cc_final: 0.7330 (mtp) REVERT: A 44 MET cc_start: 0.8935 (tpt) cc_final: 0.8702 (tpp) REVERT: A 82 MET cc_start: 0.8849 (tpt) cc_final: 0.8613 (tpt) REVERT: A 161 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7834 (p90) outliers start: 30 outliers final: 26 residues processed: 119 average time/residue: 0.2210 time to fit residues: 42.8794 Evaluate side-chains 125 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 257 CYS 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: 5.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 0.0970 chunk 61 optimal weight: 9.9990 chunk 150 optimal weight: 0.0770 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.065085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053030 restraints weight = 52647.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.055120 restraints weight = 28361.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056570 restraints weight = 18712.199| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15150 Z= 0.180 Angle : 0.561 11.337 20595 Z= 0.256 Chirality : 0.042 0.131 2290 Planarity : 0.004 0.044 2600 Dihedral : 6.677 73.356 2315 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.79 % Allowed : 10.99 % Favored : 87.22 % 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: 0.61 (0.22), residues: 635 sheet: -0.52 (0.27), residues: 335 loop : -0.23 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.003 0.000 HIS B 88 PHE 0.010 0.001 PHE A 223 TYR 0.009 0.001 TYR E 218 ARG 0.002 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2356.90 seconds wall clock time: 44 minutes 23.56 seconds (2663.56 seconds total)