Starting phenix.real_space_refine on Sat Jan 20 11:42:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ahq_11790/01_2024/7ahq_11790_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 15 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9525 2.51 5 N 2510 2.21 5 O 2895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15055 Number of models: 1 Model: "" Number of chains: 10 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: "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: "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: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'RLZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'RLZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 189 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'RLZ': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1, 'RLZ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.35, per 1000 atoms: 0.55 Number of scatterers: 15055 At special positions: 0 Unit cell: (89.76, 95.88, 190.4, 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 15 15.00 Mg 5 11.99 O 2895 8.00 N 2510 7.00 C 9525 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 2.7 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: 95 helices and 20 sheets defined 43.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.572A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (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 removed outlier: 3.506A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.795A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.732A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.534A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.712A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.595A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.852A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.789A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.124A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.572A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (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 removed outlier: 3.506A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.795A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.731A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.534A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.712A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.595A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.851A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.788A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.125A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.572A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (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 removed outlier: 3.507A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.795A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.731A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.534A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.712A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.594A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.852A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.789A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.125A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.573A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (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 removed outlier: 3.507A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.795A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.732A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.534A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.712A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.595A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.852A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.788A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.125A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.573A pdb=" N GLU E 83 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (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 removed outlier: 3.507A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.795A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.732A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.534A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 removed outlier: 3.712A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.594A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 290 through 296 removed outlier: 3.852A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.788A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.125A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.669A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.730A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.631A pdb=" N THR A 160 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 239 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.669A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.730A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.630A pdb=" N THR B 160 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.670A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.730A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.630A pdb=" N THR C 160 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.670A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 removed outlier: 3.730A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.630A pdb=" N THR D 160 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 239 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.669A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 9 " --> pdb=" O GLY E 20 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 removed outlier: 3.730A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 298 through 300 removed outlier: 3.630A pdb=" N THR E 160 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 239 through 241 450 hydrogen bonds defined for protein. 1035 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: 5.22 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2479 1.30 - 1.43: 4047 1.43 - 1.56: 8604 1.56 - 1.68: 80 1.68 - 1.81: 185 Bond restraints: 15395 Sorted by residual: bond pdb=" C31 RLZ D 405 " pdb=" C32 RLZ D 405 " ideal model delta sigma weight residual 0.228 1.527 -1.299 2.00e-02 2.50e+03 4.22e+03 bond pdb=" C31 RLZ A 404 " pdb=" C32 RLZ A 404 " ideal model delta sigma weight residual 0.228 1.527 -1.299 2.00e-02 2.50e+03 4.22e+03 bond pdb=" C31 RLZ E 401 " pdb=" C32 RLZ E 401 " ideal model delta sigma weight residual 0.228 1.526 -1.298 2.00e-02 2.50e+03 4.21e+03 bond pdb=" C31 RLZ D 401 " pdb=" C32 RLZ D 401 " ideal model delta sigma weight residual 0.228 1.526 -1.298 2.00e-02 2.50e+03 4.21e+03 bond pdb=" C31 RLZ C 401 " pdb=" C32 RLZ C 401 " ideal model delta sigma weight residual 0.228 1.526 -1.298 2.00e-02 2.50e+03 4.21e+03 ... (remaining 15390 not shown) Histogram of bond angle deviations from ideal: 82.65 - 93.26: 10 93.26 - 103.88: 345 103.88 - 114.49: 9139 114.49 - 125.10: 11126 125.10 - 135.71: 280 Bond angle restraints: 20900 Sorted by residual: angle pdb=" C28 RLZ E 401 " pdb=" C27 RLZ E 401 " pdb=" N24 RLZ E 401 " ideal model delta sigma weight residual 143.72 82.65 61.07 3.00e+00 1.11e-01 4.14e+02 angle pdb=" C28 RLZ D 401 " pdb=" C27 RLZ D 401 " pdb=" N24 RLZ D 401 " ideal model delta sigma weight residual 143.72 82.66 61.06 3.00e+00 1.11e-01 4.14e+02 angle pdb=" C28 RLZ C 401 " pdb=" C27 RLZ C 401 " pdb=" N24 RLZ C 401 " ideal model delta sigma weight residual 143.72 82.66 61.06 3.00e+00 1.11e-01 4.14e+02 angle pdb=" C28 RLZ D 405 " pdb=" C27 RLZ D 405 " pdb=" N24 RLZ D 405 " ideal model delta sigma weight residual 143.72 82.67 61.05 3.00e+00 1.11e-01 4.14e+02 angle pdb=" C28 RLZ A 404 " pdb=" C27 RLZ A 404 " pdb=" N24 RLZ A 404 " ideal model delta sigma weight residual 143.72 82.70 61.02 3.00e+00 1.11e-01 4.14e+02 ... (remaining 20895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.97: 8805 30.97 - 61.94: 250 61.94 - 92.90: 30 92.90 - 123.87: 15 123.87 - 154.84: 25 Dihedral angle restraints: 9125 sinusoidal: 3765 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 75.62 -135.63 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O1B ADP D 402 " pdb=" O3A ADP D 402 " pdb=" PB ADP D 402 " pdb=" PA ADP D 402 " ideal model delta sinusoidal sigma weight residual -60.00 75.59 -135.59 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.58 -135.58 1 2.00e+01 2.50e-03 4.11e+01 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.607: 2265 0.607 - 1.213: 0 1.213 - 1.820: 0 1.820 - 2.427: 0 2.427 - 3.033: 15 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C27 RLZ C 401 " pdb=" C28 RLZ C 401 " pdb=" C76 RLZ C 401 " pdb=" N24 RLZ C 401 " both_signs ideal model delta sigma weight residual False -0.34 2.69 -3.03 2.00e-01 2.50e+01 2.30e+02 chirality pdb=" C27 RLZ D 401 " pdb=" C28 RLZ D 401 " pdb=" C76 RLZ D 401 " pdb=" N24 RLZ D 401 " both_signs ideal model delta sigma weight residual False -0.34 2.69 -3.03 2.00e-01 2.50e+01 2.30e+02 chirality pdb=" C27 RLZ A 404 " pdb=" C28 RLZ A 404 " pdb=" C76 RLZ A 404 " pdb=" N24 RLZ A 404 " both_signs ideal model delta sigma weight residual False -0.34 2.69 -3.03 2.00e-01 2.50e+01 2.30e+02 ... (remaining 2277 not shown) Planarity restraints: 2650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 147 " 0.088 9.50e-02 1.11e+02 5.17e-02 1.48e+01 pdb=" NE ARG A 147 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 147 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG A 147 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG A 147 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 147 " -0.089 9.50e-02 1.11e+02 5.17e-02 1.47e+01 pdb=" NE ARG B 147 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 147 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG B 147 " 0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG B 147 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.089 9.50e-02 1.11e+02 5.20e-02 1.47e+01 pdb=" NE ARG C 147 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.018 2.00e-02 2.50e+03 ... (remaining 2647 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 78 2.51 - 3.11: 11975 3.11 - 3.71: 21671 3.71 - 4.30: 32901 4.30 - 4.90: 54095 Nonbonded interactions: 120720 Sorted by model distance: nonbonded pdb=" O3B ADP C 402 " pdb="MG MG C 404 " model vdw 1.918 2.170 nonbonded pdb=" O3B ADP E 402 " pdb="MG MG E 404 " model vdw 1.918 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 403 " model vdw 1.919 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 403 " model vdw 1.919 2.170 nonbonded pdb=" O3B ADP D 402 " pdb="MG MG D 404 " model vdw 1.919 2.170 ... (remaining 120715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 375) selection = (chain 'B' and resid 5 through 375) selection = (chain 'C' and resid 5 through 375) selection = (chain 'D' and resid 5 through 375) selection = (chain 'E' and resid 5 through 375) } 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: 2.030 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: 11.570 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 42.740 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.070 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.056 1.299 15395 Z= 3.586 Angle : 2.751 61.069 20900 Z= 1.028 Chirality : 0.249 3.033 2280 Planarity : 0.009 0.074 2650 Dihedral : 18.223 154.837 5695 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -2.65 (0.18), residues: 1830 helix: -2.91 (0.14), residues: 720 sheet: -0.68 (0.34), residues: 195 loop : -0.85 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP E 86 HIS 0.017 0.003 HIS C 275 PHE 0.029 0.004 PHE D 352 TYR 0.024 0.004 TYR E 294 ARG 0.064 0.012 ARG A 147 *********************** 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 156 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2827 time to fit residues: 64.5867 Evaluate side-chains 92 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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: 2.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15395 Z= 0.242 Angle : 1.112 24.829 20900 Z= 0.442 Chirality : 0.057 0.611 2280 Planarity : 0.006 0.083 2650 Dihedral : 20.878 158.601 2215 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.38 % Allowed : 3.71 % Favored : 95.91 % 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: -1.45 (0.19), residues: 1830 helix: -1.68 (0.16), residues: 735 sheet: -1.65 (0.28), residues: 240 loop : 0.21 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 86 HIS 0.008 0.001 HIS A 275 PHE 0.011 0.001 PHE C 375 TYR 0.010 0.001 TYR D 166 ARG 0.004 0.001 ARG E 210 *********************** 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 112 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.688 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 106 average time/residue: 0.2458 time to fit residues: 41.5670 Evaluate side-chains 91 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.2980 chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 114 optimal weight: 0.0020 chunk 46 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.2594 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15395 Z= 0.284 Angle : 1.050 24.731 20900 Z= 0.412 Chirality : 0.047 0.290 2280 Planarity : 0.005 0.060 2650 Dihedral : 21.665 179.740 2215 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.51 % Allowed : 6.13 % Favored : 93.35 % 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: -0.72 (0.19), residues: 1830 helix: -1.07 (0.18), residues: 735 sheet: -0.90 (0.34), residues: 185 loop : 0.38 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 86 HIS 0.007 0.001 HIS D 275 PHE 0.011 0.001 PHE D 90 TYR 0.012 0.001 TYR A 133 ARG 0.011 0.001 ARG B 95 *********************** 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 102 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.2514 time to fit residues: 39.3391 Evaluate side-chains 92 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 217 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.8166 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15395 Z= 0.303 Angle : 1.004 21.773 20900 Z= 0.396 Chirality : 0.047 0.285 2280 Planarity : 0.004 0.034 2650 Dihedral : 21.619 177.723 2215 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.02 % Allowed : 6.84 % Favored : 92.14 % 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: -0.23 (0.19), residues: 1830 helix: -0.70 (0.19), residues: 705 sheet: -0.69 (0.32), residues: 240 loop : 0.76 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 79 HIS 0.006 0.001 HIS C 275 PHE 0.010 0.001 PHE D 31 TYR 0.009 0.001 TYR B 306 ARG 0.003 0.000 ARG B 95 *********************** 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 106 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.6406 (mtm) REVERT: D 47 MET cc_start: 0.6430 (mpp) cc_final: 0.5684 (mpp) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 0.2379 time to fit residues: 39.6093 Evaluate side-chains 100 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 217 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: 1.9990 chunk 2 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 0.0170 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 overall best weight: 0.8822 ------------------------------------------------------------------------------- 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: 0.8081 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15395 Z= 0.148 Angle : 0.940 18.677 20900 Z= 0.358 Chirality : 0.045 0.291 2280 Planarity : 0.004 0.029 2650 Dihedral : 20.722 178.444 2215 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.09 % Allowed : 7.16 % Favored : 91.76 % 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: 0.25 (0.19), residues: 1830 helix: -0.23 (0.20), residues: 675 sheet: -0.68 (0.34), residues: 210 loop : 0.94 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 340 HIS 0.006 0.001 HIS C 275 PHE 0.006 0.001 PHE D 31 TYR 0.005 0.001 TYR D 306 ARG 0.004 0.000 ARG B 95 *********************** 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 110 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 270 GLU cc_start: 0.5547 (OUTLIER) cc_final: 0.4666 (mt-10) REVERT: C 47 MET cc_start: 0.7120 (mmm) cc_final: 0.6239 (mtt) REVERT: D 47 MET cc_start: 0.6517 (mpp) cc_final: 0.5500 (mpp) REVERT: E 346 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8983 (tt) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.2255 time to fit residues: 39.5800 Evaluate side-chains 104 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 0.0670 overall best weight: 5.2126 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15395 Z= 0.399 Angle : 1.023 19.751 20900 Z= 0.410 Chirality : 0.049 0.332 2280 Planarity : 0.004 0.032 2650 Dihedral : 20.630 178.830 2215 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.60 % Allowed : 7.73 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1830 helix: -0.53 (0.19), residues: 710 sheet: -0.55 (0.34), residues: 235 loop : 0.88 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 79 HIS 0.005 0.001 HIS C 275 PHE 0.012 0.001 PHE D 31 TYR 0.008 0.001 TYR C 294 ARG 0.002 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 116 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 1.635 Fit side-chains REVERT: A 270 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.4543 (mt-10) REVERT: B 47 MET cc_start: 0.7007 (mmm) cc_final: 0.6206 (mtt) REVERT: B 215 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7649 (mtmm) REVERT: C 47 MET cc_start: 0.7436 (mmm) cc_final: 0.6320 (mtt) REVERT: C 305 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6575 (mtm) REVERT: D 346 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8855 (tt) REVERT: E 346 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9021 (tt) outliers start: 25 outliers final: 12 residues processed: 112 average time/residue: 0.2206 time to fit residues: 40.1687 Evaluate side-chains 106 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 346 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8152 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15395 Z= 0.213 Angle : 0.957 19.800 20900 Z= 0.370 Chirality : 0.046 0.303 2280 Planarity : 0.004 0.033 2650 Dihedral : 20.482 179.046 2215 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.47 % Allowed : 8.31 % Favored : 90.22 % 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: 0.14 (0.20), residues: 1830 helix: -0.34 (0.19), residues: 710 sheet: -0.44 (0.35), residues: 235 loop : 0.91 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 79 HIS 0.006 0.001 HIS C 275 PHE 0.012 0.001 PHE C 31 TYR 0.006 0.001 TYR C 294 ARG 0.002 0.000 ARG A 210 *********************** 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 115 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 270 GLU cc_start: 0.5521 (OUTLIER) cc_final: 0.4447 (mt-10) REVERT: C 47 MET cc_start: 0.7294 (mmm) cc_final: 0.6921 (mmm) REVERT: D 346 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8845 (tt) REVERT: E 346 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8983 (tt) outliers start: 23 outliers final: 13 residues processed: 113 average time/residue: 0.2359 time to fit residues: 42.9479 Evaluate side-chains 105 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 346 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 0.0870 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 GLN D 162 ASN E 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15395 Z= 0.142 Angle : 0.927 19.457 20900 Z= 0.352 Chirality : 0.045 0.293 2280 Planarity : 0.004 0.033 2650 Dihedral : 20.160 179.306 2215 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.96 % Allowed : 8.95 % Favored : 90.10 % 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: 0.40 (0.20), residues: 1830 helix: -0.06 (0.20), residues: 710 sheet: -0.23 (0.35), residues: 235 loop : 0.96 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 79 HIS 0.006 0.001 HIS C 275 PHE 0.010 0.001 PHE C 31 TYR 0.007 0.001 TYR C 337 ARG 0.003 0.000 ARG B 95 *********************** 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 113 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.800 Fit side-chains revert: symmetry clash REVERT: A 270 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.4587 (mt-10) REVERT: D 82 MET cc_start: 0.7620 (tpp) cc_final: 0.7214 (tpt) REVERT: D 346 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8812 (tt) outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 0.2255 time to fit residues: 40.8118 Evaluate side-chains 98 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 346 LEU 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: 9.9990 chunk 166 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 72 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15395 Z= 0.262 Angle : 0.975 19.741 20900 Z= 0.380 Chirality : 0.047 0.314 2280 Planarity : 0.004 0.035 2650 Dihedral : 20.251 177.216 2215 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.09 % Allowed : 8.56 % Favored : 90.35 % 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: 0.43 (0.20), residues: 1830 helix: -0.07 (0.19), residues: 710 sheet: -0.17 (0.36), residues: 235 loop : 1.00 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 79 HIS 0.006 0.001 HIS C 275 PHE 0.012 0.001 PHE C 31 TYR 0.011 0.001 TYR C 306 ARG 0.002 0.000 ARG A 210 *********************** 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 108 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.752 Fit side-chains REVERT: A 44 MET cc_start: 0.6942 (mmm) cc_final: 0.6630 (mmm) REVERT: A 270 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.4535 (mt-10) REVERT: B 215 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7703 (mtmm) REVERT: C 47 MET cc_start: 0.6296 (mpp) cc_final: 0.6084 (mpp) REVERT: D 82 MET cc_start: 0.7818 (tpp) cc_final: 0.7417 (tpt) REVERT: D 346 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8892 (tt) REVERT: D 355 MET cc_start: 0.7793 (mmm) cc_final: 0.7568 (mmm) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 0.2169 time to fit residues: 37.8228 Evaluate side-chains 103 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 184 optimal weight: 0.0670 chunk 169 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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: 0.8124 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15395 Z= 0.193 Angle : 0.945 19.963 20900 Z= 0.363 Chirality : 0.046 0.297 2280 Planarity : 0.004 0.034 2650 Dihedral : 20.103 177.873 2215 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.89 % Allowed : 8.82 % Favored : 90.29 % 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: 0.53 (0.20), residues: 1830 helix: 0.08 (0.20), residues: 710 sheet: -0.11 (0.35), residues: 235 loop : 0.99 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 79 HIS 0.006 0.001 HIS C 275 PHE 0.011 0.001 PHE C 31 TYR 0.010 0.001 TYR E 279 ARG 0.002 0.000 ARG D 210 ********************** 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 105 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.724 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.6858 (mmm) cc_final: 0.6654 (mmm) REVERT: A 270 GLU cc_start: 0.5652 (OUTLIER) cc_final: 0.4660 (mt-10) REVERT: D 82 MET cc_start: 0.7733 (tpp) cc_final: 0.7330 (tpt) REVERT: D 346 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8855 (tt) outliers start: 14 outliers final: 11 residues processed: 104 average time/residue: 0.2411 time to fit residues: 40.3679 Evaluate side-chains 102 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 132 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 0.0770 chunk 61 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.042088 restraints weight = 68132.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.044017 restraints weight = 33013.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.045358 restraints weight = 19976.308| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15395 Z= 0.225 Angle : 0.955 20.054 20900 Z= 0.369 Chirality : 0.046 0.309 2280 Planarity : 0.004 0.037 2650 Dihedral : 20.029 177.604 2215 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.15 % Allowed : 8.95 % Favored : 89.90 % 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: 0.55 (0.20), residues: 1830 helix: 0.12 (0.20), residues: 710 sheet: -0.11 (0.35), residues: 235 loop : 0.98 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 79 HIS 0.006 0.001 HIS C 275 PHE 0.011 0.001 PHE C 31 TYR 0.007 0.001 TYR E 306 ARG 0.002 0.000 ARG A 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2306.45 seconds wall clock time: 43 minutes 37.13 seconds (2617.13 seconds total)