Starting phenix.real_space_refine on Sun Dec 10 16:08:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/12_2023/5ooc_3836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/12_2023/5ooc_3836.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/12_2023/5ooc_3836_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/5ooc_3836/12_2023/5ooc_3836_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/12_2023/5ooc_3836_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/12_2023/5ooc_3836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/12_2023/5ooc_3836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/12_2023/5ooc_3836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ooc_3836/12_2023/5ooc_3836_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= 0.022 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 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "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 TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "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 TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "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 TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "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 TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "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 TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14885 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, '9ZK': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.95, per 1000 atoms: 0.53 Number of scatterers: 14885 At special positions: 0 Unit cell: (100.32, 85.5, 190.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2845 8.00 N 2495 7.00 C 9425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 2.9 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 20 sheets defined 44.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... 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 92 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.126A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.508A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 5.311A 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 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 4.485A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.260A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.127A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.508A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 5.312A 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 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 4.485A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (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 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.261A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 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 92 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.127A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.509A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 removed outlier: 5.312A 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 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.484A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (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 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.261A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.127A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.508A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 5.313A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.485A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (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 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.261A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 4.127A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.508A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 5.311A 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 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.485A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (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 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.261A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 355 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: 6.565A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.761A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.564A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.761A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.564A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.760A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.564A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.761A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.565A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.761A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 555 hydrogen bonds defined for protein. 1335 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: 4.41 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2455 1.28 - 1.41: 3835 1.41 - 1.54: 8721 1.54 - 1.68: 24 1.68 - 1.81: 185 Bond restraints: 15220 Sorted by residual: bond pdb=" C07 9ZK D 403 " pdb=" C08 9ZK D 403 " ideal model delta sigma weight residual 2.679 1.510 1.169 2.00e-02 2.50e+03 3.41e+03 bond pdb=" C07 9ZK A 404 " pdb=" C08 9ZK A 404 " ideal model delta sigma weight residual 2.679 1.511 1.168 2.00e-02 2.50e+03 3.41e+03 bond pdb=" C07 9ZK A 402 " pdb=" C08 9ZK A 402 " ideal model delta sigma weight residual 2.679 1.511 1.168 2.00e-02 2.50e+03 3.41e+03 bond pdb=" C07 9ZK C 403 " pdb=" C08 9ZK C 403 " ideal model delta sigma weight residual 2.679 1.511 1.168 2.00e-02 2.50e+03 3.41e+03 bond pdb=" C07 9ZK B 403 " pdb=" C08 9ZK B 403 " ideal model delta sigma weight residual 2.679 1.511 1.168 2.00e-02 2.50e+03 3.41e+03 ... (remaining 15215 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.41: 479 105.41 - 113.14: 8139 113.14 - 120.87: 7657 120.87 - 128.59: 4275 128.59 - 136.32: 110 Bond angle restraints: 20660 Sorted by residual: angle pdb=" C09 9ZK C 403 " pdb=" C11 9ZK C 403 " pdb=" C12 9ZK C 403 " ideal model delta sigma weight residual 180.00 111.17 68.83 3.00e+00 1.11e-01 5.26e+02 angle pdb=" C09 9ZK A 404 " pdb=" C11 9ZK A 404 " pdb=" C12 9ZK A 404 " ideal model delta sigma weight residual 180.00 111.18 68.82 3.00e+00 1.11e-01 5.26e+02 angle pdb=" C09 9ZK B 403 " pdb=" C11 9ZK B 403 " pdb=" C12 9ZK B 403 " ideal model delta sigma weight residual 180.00 111.18 68.82 3.00e+00 1.11e-01 5.26e+02 angle pdb=" C09 9ZK A 402 " pdb=" C11 9ZK A 402 " pdb=" C12 9ZK A 402 " ideal model delta sigma weight residual 180.00 111.24 68.76 3.00e+00 1.11e-01 5.25e+02 angle pdb=" C09 9ZK D 403 " pdb=" C11 9ZK D 403 " pdb=" C12 9ZK D 403 " ideal model delta sigma weight residual 180.00 111.24 68.76 3.00e+00 1.11e-01 5.25e+02 ... (remaining 20655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 8900 35.02 - 70.03: 120 70.03 - 105.05: 35 105.05 - 140.06: 15 140.06 - 175.08: 25 Dihedral angle restraints: 9095 sinusoidal: 3735 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.22 -149.23 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.20 -149.20 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.20 -149.20 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 9092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.835: 2270 0.835 - 1.669: 5 1.669 - 2.504: 0 2.504 - 3.339: 0 3.339 - 4.173: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C16 9ZK D 403 " pdb=" C17 9ZK D 403 " pdb=" C22 9ZK D 403 " pdb=" N15 9ZK D 403 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.17 2.00e-01 2.50e+01 4.35e+02 chirality pdb=" C16 9ZK A 402 " pdb=" C17 9ZK A 402 " pdb=" C22 9ZK A 402 " pdb=" N15 9ZK A 402 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.17 2.00e-01 2.50e+01 4.35e+02 chirality pdb=" C16 9ZK C 403 " pdb=" C17 9ZK C 403 " pdb=" C22 9ZK C 403 " pdb=" N15 9ZK C 403 " both_signs ideal model delta sigma weight residual False 1.76 -2.41 4.17 2.00e-01 2.50e+01 4.35e+02 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO A 164 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO B 164 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.097 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C 164 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.075 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 175 2.62 - 3.19: 14984 3.19 - 3.76: 23185 3.76 - 4.33: 34919 4.33 - 4.90: 53410 Nonbonded interactions: 126673 Sorted by model distance: nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 403 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.051 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 2.051 2.170 ... (remaining 126668 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 or resid 401)) selection = (chain 'B' and (resid 5 through 375 or resid 401)) selection = (chain 'C' and (resid 5 through 375 or resid 401)) selection = (chain 'D' and (resid 5 through 375 or resid 401)) selection = (chain 'E' and (resid 5 through 375 or resid 401)) } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.500 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 40.760 Find NCS groups from input model: 1.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.049 1.169 15220 Z= 3.142 Angle : 3.107 68.833 20660 Z= 1.335 Chirality : 0.220 4.173 2280 Planarity : 0.018 0.147 2630 Dihedral : 17.808 175.080 5665 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 2.73 % Allowed : 4.37 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -1.43 (0.20), residues: 1830 helix: -1.31 (0.16), residues: 715 sheet: -0.73 (0.26), residues: 310 loop : -0.45 (0.26), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP C 340 HIS 0.007 0.002 HIS B 88 PHE 0.010 0.003 PHE C 90 TYR 0.021 0.004 TYR B 198 ARG 0.005 0.001 ARG D 39 *********************** 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 500 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.3136 time to fit residues: 218.2207 Evaluate side-chains 223 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN E 246 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15220 Z= 0.223 Angle : 1.594 33.050 20660 Z= 0.592 Chirality : 0.048 0.316 2280 Planarity : 0.009 0.061 2630 Dihedral : 24.658 179.948 2185 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 1.09 % Allowed : 2.24 % Favored : 96.67 % Rotamer: Outliers : 1.60 % Allowed : 8.75 % Favored : 89.65 % 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: -0.20 (0.20), residues: 1830 helix: 0.34 (0.19), residues: 760 sheet: -0.66 (0.27), residues: 280 loop : -0.21 (0.25), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 340 HIS 0.007 0.001 HIS A 101 PHE 0.007 0.001 PHE E 127 TYR 0.020 0.001 TYR A 166 ARG 0.010 0.001 ARG B 147 *********************** 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 343 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 318 time to evaluate : 1.817 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 338 average time/residue: 0.2433 time to fit residues: 125.3655 Evaluate side-chains 246 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1514 time to fit residues: 6.5291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 114 optimal weight: 0.0670 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS E 115 ASN E 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15220 Z= 0.234 Angle : 1.553 32.504 20660 Z= 0.571 Chirality : 0.046 0.197 2280 Planarity : 0.007 0.054 2630 Dihedral : 23.019 172.413 2185 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.55 % Favored : 95.36 % Rotamer: Outliers : 2.30 % Allowed : 12.08 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1830 helix: 0.57 (0.19), residues: 770 sheet: -0.27 (0.30), residues: 250 loop : -0.17 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 86 HIS 0.008 0.001 HIS C 40 PHE 0.026 0.001 PHE A 352 TYR 0.015 0.001 TYR A 166 ARG 0.009 0.001 ARG D 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 322 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 286 time to evaluate : 1.805 Fit side-chains outliers start: 36 outliers final: 15 residues processed: 307 average time/residue: 0.2466 time to fit residues: 117.1323 Evaluate side-chains 236 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1419 time to fit residues: 6.2621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN B 49 GLN B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN E 115 ASN E 252 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15220 Z= 0.175 Angle : 1.520 32.344 20660 Z= 0.552 Chirality : 0.044 0.157 2280 Planarity : 0.005 0.050 2630 Dihedral : 22.658 173.082 2185 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 1.09 % Allowed : 2.68 % Favored : 96.23 % Rotamer: Outliers : 2.04 % Allowed : 14.06 % Favored : 83.90 % 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: 0.26 (0.20), residues: 1830 helix: 0.76 (0.19), residues: 770 sheet: -0.08 (0.31), residues: 250 loop : -0.18 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 86 HIS 0.006 0.001 HIS C 40 PHE 0.024 0.001 PHE A 352 TYR 0.019 0.001 TYR A 166 ARG 0.004 0.000 ARG E 256 *********************** 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 283 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 1.757 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 263 average time/residue: 0.2211 time to fit residues: 92.1446 Evaluate side-chains 243 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1427 time to fit residues: 7.2923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 0.3980 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 0.1980 chunk 123 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15220 Z= 0.408 Angle : 1.577 32.474 20660 Z= 0.590 Chirality : 0.050 0.310 2280 Planarity : 0.006 0.047 2630 Dihedral : 21.992 172.524 2185 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 1.09 % Allowed : 4.32 % Favored : 94.59 % Rotamer: Outliers : 2.43 % Allowed : 15.40 % Favored : 82.17 % 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: 0.00 (0.19), residues: 1830 helix: 0.56 (0.19), residues: 730 sheet: -0.02 (0.31), residues: 285 loop : -0.38 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 79 HIS 0.008 0.001 HIS A 101 PHE 0.028 0.002 PHE A 352 TYR 0.027 0.002 TYR A 166 ARG 0.004 0.001 ARG E 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 277 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 239 time to evaluate : 1.552 Fit side-chains outliers start: 38 outliers final: 23 residues processed: 265 average time/residue: 0.2324 time to fit residues: 94.9575 Evaluate side-chains 237 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 1.791 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1444 time to fit residues: 8.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 115 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15220 Z= 0.212 Angle : 1.533 32.261 20660 Z= 0.559 Chirality : 0.045 0.225 2280 Planarity : 0.005 0.045 2630 Dihedral : 21.779 179.125 2185 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.22 % Favored : 95.68 % Rotamer: Outliers : 0.96 % Allowed : 17.51 % Favored : 81.53 % 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: -0.07 (0.20), residues: 1830 helix: 0.52 (0.19), residues: 760 sheet: -0.28 (0.29), residues: 310 loop : -0.37 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 86 HIS 0.007 0.001 HIS A 101 PHE 0.028 0.001 PHE A 352 TYR 0.019 0.001 TYR A 166 ARG 0.006 0.000 ARG B 95 *********************** 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 248 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 1.530 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 239 average time/residue: 0.2308 time to fit residues: 86.5391 Evaluate side-chains 222 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 213 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1716 time to fit residues: 4.8921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN B 162 ASN C 41 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15220 Z= 0.205 Angle : 1.536 32.283 20660 Z= 0.561 Chirality : 0.046 0.226 2280 Planarity : 0.005 0.044 2630 Dihedral : 21.640 179.851 2185 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 1.04 % Allowed : 3.72 % Favored : 95.25 % Rotamer: Outliers : 1.09 % Allowed : 18.15 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1830 helix: 0.49 (0.19), residues: 760 sheet: -0.27 (0.30), residues: 310 loop : -0.41 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 86 HIS 0.007 0.001 HIS A 101 PHE 0.030 0.001 PHE A 352 TYR 0.020 0.001 TYR A 166 ARG 0.005 0.000 ARG C 372 *********************** 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 231 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 214 time to evaluate : 1.605 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 224 average time/residue: 0.2377 time to fit residues: 83.7726 Evaluate side-chains 210 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1442 time to fit residues: 4.0519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 0.0030 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15220 Z= 0.163 Angle : 1.523 32.238 20660 Z= 0.553 Chirality : 0.045 0.208 2280 Planarity : 0.004 0.044 2630 Dihedral : 21.368 178.565 2185 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 1.04 % Allowed : 3.11 % Favored : 95.85 % Rotamer: Outliers : 0.83 % Allowed : 18.85 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1830 helix: 0.68 (0.19), residues: 750 sheet: -0.49 (0.29), residues: 335 loop : -0.38 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 86 HIS 0.006 0.001 HIS A 101 PHE 0.031 0.001 PHE A 352 TYR 0.014 0.001 TYR A 166 ARG 0.006 0.000 ARG C 372 *********************** 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 230 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 1.689 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 224 average time/residue: 0.2245 time to fit residues: 80.0044 Evaluate side-chains 209 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 204 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1399 time to fit residues: 3.7737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 10.0000 chunk 155 optimal weight: 0.3980 chunk 166 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 354 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15220 Z= 0.372 Angle : 1.564 32.498 20660 Z= 0.580 Chirality : 0.049 0.288 2280 Planarity : 0.005 0.043 2630 Dihedral : 21.157 175.373 2185 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.93 % Allowed : 4.92 % Favored : 94.15 % Rotamer: Outliers : 0.89 % Allowed : 19.30 % Favored : 79.81 % 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: -0.31 (0.19), residues: 1830 helix: 0.39 (0.19), residues: 745 sheet: -0.47 (0.29), residues: 335 loop : -0.53 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 79 HIS 0.007 0.001 HIS D 161 PHE 0.033 0.002 PHE A 352 TYR 0.016 0.002 TYR A 166 ARG 0.005 0.001 ARG C 372 *********************** 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 223 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 1.728 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 217 average time/residue: 0.2407 time to fit residues: 83.1909 Evaluate side-chains 201 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1400 time to fit residues: 4.5836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 354 GLN C 12 ASN C 41 GLN C 252 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15220 Z= 0.173 Angle : 1.527 32.305 20660 Z= 0.557 Chirality : 0.045 0.208 2280 Planarity : 0.005 0.044 2630 Dihedral : 20.842 179.711 2185 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.06 % Favored : 96.07 % Rotamer: Outliers : 0.32 % Allowed : 19.87 % Favored : 79.81 % 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: -0.20 (0.20), residues: 1830 helix: 0.53 (0.19), residues: 750 sheet: -0.32 (0.29), residues: 330 loop : -0.60 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 86 HIS 0.005 0.001 HIS A 101 PHE 0.032 0.001 PHE A 352 TYR 0.015 0.001 TYR A 166 ARG 0.007 0.000 ARG C 372 ********************** 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 228 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 1.807 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 226 average time/residue: 0.2510 time to fit residues: 88.2744 Evaluate side-chains 209 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1384 time to fit residues: 2.7909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 41 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.098221 restraints weight = 23470.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.101265 restraints weight = 11955.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103278 restraints weight = 7423.354| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15220 Z= 0.237 Angle : 1.532 32.273 20660 Z= 0.560 Chirality : 0.046 0.233 2280 Planarity : 0.005 0.045 2630 Dihedral : 20.718 176.040 2185 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.77 % Allowed : 4.10 % Favored : 95.14 % Rotamer: Outliers : 0.26 % Allowed : 20.00 % Favored : 79.74 % 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: 0.53 (0.19), residues: 750 sheet: -0.30 (0.29), residues: 330 loop : -0.62 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 86 HIS 0.005 0.001 HIS E 87 PHE 0.028 0.001 PHE A 352 TYR 0.022 0.001 TYR A 166 ARG 0.009 0.000 ARG C 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2860.18 seconds wall clock time: 53 minutes 9.87 seconds (3189.87 seconds total)