Starting phenix.real_space_refine on Sat Nov 18 09:23:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/11_2023/8f8t_28936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/11_2023/8f8t_28936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/11_2023/8f8t_28936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/11_2023/8f8t_28936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/11_2023/8f8t_28936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/11_2023/8f8t_28936_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 14 5.49 5 Mg 7 5.21 5 S 153 5.16 5 C 14122 2.51 5 N 3785 2.21 5 O 4312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 22393 Number of models: 1 Model: "" Number of chains: 15 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: "T" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1843 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 14, 'TRANS': 215} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" 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: 11.68, per 1000 atoms: 0.52 Number of scatterers: 22393 At special positions: 0 Unit cell: (91.8, 104.76, 246.24, 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 153 16.00 P 14 15.00 Mg 7 11.99 O 4312 8.00 N 3785 7.00 C 14122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.83 Conformation dependent library (CDL) restraints added in 3.9 seconds 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 35 sheets defined 43.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... 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 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.927A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.543A 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 289 through 294 Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 347 removed outlier: 5.867A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 374 removed outlier: 4.141A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N CYS A 374 " --> pdb=" O HIS A 371 " (cutoff:3.500A) 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 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: 4.045A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.702A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.927A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 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 296 removed outlier: 3.598A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 295 " --> pdb=" O ASP B 292 " (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: 5.391A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 369 through 373 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 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 144 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: 3.998A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.795A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.932A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 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 296 removed outlier: 3.586A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 295 " --> pdb=" O ASP C 292 " (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: 3.738A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 369 through 373 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 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 144 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: 4.087A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.792A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.951A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 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 296 removed outlier: 3.599A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 295 " --> pdb=" O ASP D 292 " (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: 3.738A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 373 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 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 144 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: 4.118A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.776A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.895A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 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 296 removed outlier: 3.584A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 295 " --> pdb=" O ASP E 292 " (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: 3.725A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 196 removed outlier: 4.073A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.805A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.923A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 296 removed outlier: 4.728A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 348 removed outlier: 3.709A pdb=" N SER F 338 " --> pdb=" O ARG F 335 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 196 removed outlier: 4.116A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 removed outlier: 3.814A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 252 through 256 removed outlier: 3.937A pdb=" N ARG G 256 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 261 Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 287 through 296 removed outlier: 3.582A pdb=" N ARG G 290 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS G 291 " --> pdb=" O ASP G 288 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA G 295 " --> pdb=" O ASP G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 348 removed outlier: 3.746A pdb=" N SER G 338 " --> pdb=" O ARG G 335 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA G 347 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'T' and resid 64 through 76 Processing helix chain 'T' and resid 183 through 191 Processing helix chain 'T' and resid 210 through 221 removed outlier: 3.652A pdb=" N LYS T 221 " --> pdb=" O ALA T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 238 through 248 Processing helix chain 'T' and resid 266 through 278 removed outlier: 3.682A pdb=" N LEU T 276 " --> pdb=" O LEU T 272 " (cutoff:3.500A) Proline residue: T 277 - end of helix Processing helix chain 'T' and resid 296 through 308 removed outlier: 3.646A pdb=" N LYS T 308 " --> pdb=" O SER T 304 " (cutoff:3.500A) Processing helix chain 'T' and resid 322 through 345 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.806A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.379A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.120A 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 8 through 12 Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= H, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.245A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= K, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= L, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= M, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.371A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= O, first strand: chain 'D' and resid 8 through 12 Processing sheet with id= P, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= Q, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= R, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.285A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= T, first strand: chain 'E' and resid 8 through 12 Processing sheet with id= U, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= V, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= W, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.322A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= Y, first strand: chain 'F' and resid 8 through 12 Processing sheet with id= Z, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= AA, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= AB, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.311A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= AD, first strand: chain 'G' and resid 8 through 12 Processing sheet with id= AE, first strand: chain 'G' and resid 35 through 38 Processing sheet with id= AF, first strand: chain 'G' and resid 103 through 107 Processing sheet with id= AG, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.391A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 238 through 241 Processing sheet with id= AI, first strand: chain 'T' and resid 199 through 201 removed outlier: 6.131A pdb=" N LYS T 228 " --> pdb=" O VAL T 200 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR T 256 " --> pdb=" O PHE T 229 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU T 284 " --> pdb=" O LEU T 257 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS T 314 " --> pdb=" O MET T 285 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI 823 hydrogen bonds defined for protein. 2022 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: 7.33 Time building geometry restraints manager: 8.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6853 1.34 - 1.46: 5052 1.46 - 1.58: 10674 1.58 - 1.70: 21 1.70 - 1.82: 271 Bond restraints: 22871 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 22866 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.77: 889 106.77 - 114.12: 12770 114.12 - 121.48: 11247 121.48 - 128.83: 5972 128.83 - 136.19: 149 Bond angle restraints: 31027 Sorted by residual: angle pdb=" C GLY F 46 " pdb=" N MET F 47 " pdb=" CA MET F 47 " ideal model delta sigma weight residual 122.08 128.79 -6.71 1.47e+00 4.63e-01 2.09e+01 angle pdb=" C ARG B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 122.06 113.75 8.31 1.86e+00 2.89e-01 2.00e+01 angle pdb=" C GLY E 46 " pdb=" N MET E 47 " pdb=" CA MET E 47 " ideal model delta sigma weight residual 122.08 128.65 -6.57 1.47e+00 4.63e-01 2.00e+01 angle pdb=" C ASP A 286 " pdb=" N ILE A 287 " pdb=" CA ILE A 287 " ideal model delta sigma weight residual 120.53 126.77 -6.24 1.41e+00 5.03e-01 1.96e+01 angle pdb=" C GLY G 46 " pdb=" N MET G 47 " pdb=" CA MET G 47 " ideal model delta sigma weight residual 122.08 128.55 -6.47 1.47e+00 4.63e-01 1.94e+01 ... (remaining 31022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 13441 35.36 - 70.73: 350 70.73 - 106.09: 11 106.09 - 141.45: 6 141.45 - 176.81: 6 Dihedral angle restraints: 13814 sinusoidal: 5615 harmonic: 8199 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.19 176.81 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.42 176.58 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.76 176.25 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 13811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2662 0.065 - 0.130: 671 0.130 - 0.195: 105 0.195 - 0.260: 9 0.260 - 0.325: 2 Chirality restraints: 3449 Sorted by residual: chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA CYS A 257 " pdb=" N CYS A 257 " pdb=" C CYS A 257 " pdb=" CB CYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE T 231 " pdb=" CA ILE T 231 " pdb=" CG1 ILE T 231 " pdb=" CG2 ILE T 231 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3446 not shown) Planarity restraints: 3975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 335 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C ARG B 335 " -0.080 2.00e-02 2.50e+03 pdb=" O ARG B 335 " 0.030 2.00e-02 2.50e+03 pdb=" N LYS B 336 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 49 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" CD GLN A 49 " -0.078 2.00e-02 2.50e+03 pdb=" OE1 GLN A 49 " 0.030 2.00e-02 2.50e+03 pdb=" NE2 GLN A 49 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 291 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C LYS A 291 " -0.076 2.00e-02 2.50e+03 pdb=" O LYS A 291 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP A 292 " 0.025 2.00e-02 2.50e+03 ... (remaining 3972 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 263 2.66 - 3.22: 19082 3.22 - 3.78: 34698 3.78 - 4.34: 49161 4.34 - 4.90: 80341 Nonbonded interactions: 183545 Sorted by model distance: nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.110 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.110 2.170 nonbonded pdb=" O1B ADP G 401 " pdb="MG MG G 402 " model vdw 2.112 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.123 2.170 ... (remaining 183540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'F' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'G' and (resid 5 through 375 or resid 401 through 402)) } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.000 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: 0.030 Extract box with map and model: 14.310 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 57.440 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.160 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.005 0.078 22871 Z= 0.326 Angle : 0.926 9.113 31027 Z= 0.525 Chirality : 0.057 0.325 3449 Planarity : 0.008 0.068 3975 Dihedral : 15.119 176.815 8558 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.58 % Allowed : 6.65 % Favored : 89.77 % 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: -0.20 (0.16), residues: 2794 helix: -0.24 (0.15), residues: 1161 sheet: 0.31 (0.23), residues: 502 loop : 0.01 (0.20), residues: 1131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 317 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 6 residues processed: 392 average time/residue: 0.3948 time to fit residues: 228.8094 Evaluate side-chains 174 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 2.611 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2531 time to fit residues: 5.8417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 164 optimal weight: 0.0570 chunk 256 optimal weight: 8.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN D 41 GLN D 59 GLN D 115 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN F 371 HIS G 41 GLN G 59 GLN G 296 ASN ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 318 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22871 Z= 0.305 Angle : 0.621 9.538 31027 Z= 0.302 Chirality : 0.045 0.164 3449 Planarity : 0.005 0.055 3975 Dihedral : 9.270 154.273 3172 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.29 % Allowed : 10.85 % Favored : 87.86 % 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: 0.64 (0.16), residues: 2794 helix: 0.67 (0.16), residues: 1154 sheet: 0.55 (0.22), residues: 496 loop : 0.32 (0.20), residues: 1144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 194 average time/residue: 0.3445 time to fit residues: 110.2944 Evaluate side-chains 173 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 2.817 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2240 time to fit residues: 11.2805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 0.2980 chunk 213 optimal weight: 7.9990 chunk 174 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 256 optimal weight: 8.9990 chunk 277 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 254 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN C 59 GLN D 41 GLN D 115 ASN E 115 ASN G 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22871 Z= 0.137 Angle : 0.532 9.536 31027 Z= 0.252 Chirality : 0.043 0.149 3449 Planarity : 0.004 0.053 3975 Dihedral : 7.330 122.172 3172 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.58 % Allowed : 11.81 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2794 helix: 0.94 (0.16), residues: 1143 sheet: 0.57 (0.22), residues: 516 loop : 0.55 (0.21), residues: 1135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 174 average time/residue: 0.3228 time to fit residues: 91.9228 Evaluate side-chains 156 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 2.713 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2004 time to fit residues: 4.7283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 172 optimal weight: 0.0570 chunk 257 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN G 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22871 Z= 0.200 Angle : 0.546 8.303 31027 Z= 0.256 Chirality : 0.043 0.151 3449 Planarity : 0.004 0.050 3975 Dihedral : 5.947 87.829 3172 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.71 % Allowed : 11.85 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2794 helix: 1.02 (0.16), residues: 1143 sheet: 0.62 (0.22), residues: 519 loop : 0.58 (0.21), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 172 average time/residue: 0.3284 time to fit residues: 92.0398 Evaluate side-chains 159 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 2.410 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1885 time to fit residues: 5.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 232 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 0.0870 chunk 244 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 115 ASN E 12 ASN G 296 ASN ** T 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22871 Z= 0.301 Angle : 0.587 9.399 31027 Z= 0.278 Chirality : 0.045 0.265 3449 Planarity : 0.004 0.051 3975 Dihedral : 5.878 80.074 3172 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.04 % Allowed : 12.60 % Favored : 86.36 % 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: 0.94 (0.17), residues: 2794 helix: 0.96 (0.16), residues: 1144 sheet: 0.49 (0.22), residues: 524 loop : 0.55 (0.21), residues: 1126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 180 average time/residue: 0.3248 time to fit residues: 95.9431 Evaluate side-chains 163 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 2.697 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2069 time to fit residues: 7.8426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN D 115 ASN D 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** T 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22871 Z= 0.206 Angle : 0.551 9.928 31027 Z= 0.258 Chirality : 0.044 0.206 3449 Planarity : 0.004 0.050 3975 Dihedral : 5.548 74.569 3172 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.37 % Allowed : 13.10 % Favored : 86.53 % 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: 1.02 (0.17), residues: 2794 helix: 1.04 (0.16), residues: 1138 sheet: 0.51 (0.23), residues: 524 loop : 0.60 (0.21), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 159 average time/residue: 0.3271 time to fit residues: 84.4723 Evaluate side-chains 153 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2197 time to fit residues: 4.9877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 155 optimal weight: 0.0370 chunk 199 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 115 ASN E 12 ASN G 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22871 Z= 0.325 Angle : 0.601 10.990 31027 Z= 0.284 Chirality : 0.045 0.204 3449 Planarity : 0.004 0.048 3975 Dihedral : 5.735 80.304 3172 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.75 % Allowed : 13.14 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2794 helix: 0.92 (0.16), residues: 1146 sheet: 0.48 (0.23), residues: 510 loop : 0.39 (0.20), residues: 1138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 161 average time/residue: 0.3470 time to fit residues: 91.3302 Evaluate side-chains 157 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2141 time to fit residues: 6.6801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22871 Z= 0.227 Angle : 0.566 11.561 31027 Z= 0.264 Chirality : 0.044 0.200 3449 Planarity : 0.004 0.048 3975 Dihedral : 5.505 74.963 3172 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.29 % Allowed : 13.43 % Favored : 86.28 % 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: 0.93 (0.17), residues: 2794 helix: 1.04 (0.16), residues: 1136 sheet: 0.48 (0.23), residues: 510 loop : 0.44 (0.20), residues: 1148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 159 average time/residue: 0.3340 time to fit residues: 86.6107 Evaluate side-chains 149 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 2.929 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2411 time to fit residues: 4.2146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22871 Z= 0.294 Angle : 0.592 12.130 31027 Z= 0.279 Chirality : 0.045 0.209 3449 Planarity : 0.004 0.048 3975 Dihedral : 5.560 76.830 3172 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.21 % Allowed : 13.51 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2794 helix: 0.90 (0.16), residues: 1153 sheet: 0.46 (0.23), residues: 509 loop : 0.40 (0.20), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 153 average time/residue: 0.3251 time to fit residues: 82.8948 Evaluate side-chains 146 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 127 optimal weight: 0.3980 chunk 186 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 115 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22871 Z= 0.374 Angle : 0.641 12.501 31027 Z= 0.303 Chirality : 0.046 0.215 3449 Planarity : 0.004 0.047 3975 Dihedral : 5.746 81.347 3172 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.04 % Allowed : 13.97 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2794 helix: 0.87 (0.16), residues: 1143 sheet: 0.40 (0.23), residues: 509 loop : 0.26 (0.20), residues: 1142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 3.618 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.3322 time to fit residues: 81.7178 Evaluate side-chains 148 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.666 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 2.9990 chunk 238 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 115 ASN G 296 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.068097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.049901 restraints weight = 70331.156| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.36 r_work: 0.2666 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22871 Z= 0.168 Angle : 0.574 12.054 31027 Z= 0.265 Chirality : 0.043 0.208 3449 Planarity : 0.004 0.048 3975 Dihedral : 5.370 70.657 3172 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % 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: 0.93 (0.17), residues: 2794 helix: 1.02 (0.16), residues: 1139 sheet: 0.49 (0.23), residues: 509 loop : 0.45 (0.20), residues: 1146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4026.11 seconds wall clock time: 74 minutes 40.27 seconds (4480.27 seconds total)