Starting phenix.real_space_refine on Sun Feb 18 17:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/02_2024/8f8t_28936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/02_2024/8f8t_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_28936/02_2024/8f8t_28936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/02_2024/8f8t_28936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/02_2024/8f8t_28936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8t_28936/02_2024/8f8t_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 11.44, per 1000 atoms: 0.51 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: 8.06 Conformation dependent library (CDL) restraints added in 4.2 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: 4.55 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: 8.51 Time building geometry restraints manager: 8.81 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: 3.960 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: 0.020 Extract box with map and model: 14.550 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 60.290 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.190 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: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.680 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 356 HIS 0.011 0.001 HIS A 87 PHE 0.020 0.002 PHE A 90 TYR 0.024 0.002 TYR A 362 ARG 0.006 0.001 ARG A 210 *********************** 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 : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: -0.2890 (OUTLIER) cc_final: -0.3233 (t) REVERT: A 82 MET cc_start: 0.8998 (tpt) cc_final: 0.8337 (tpp) REVERT: A 118 LYS cc_start: 0.9268 (tptt) cc_final: 0.8982 (tppt) REVERT: A 121 GLN cc_start: 0.9387 (tt0) cc_final: 0.8905 (tm-30) REVERT: A 132 MET cc_start: 0.9014 (ppp) cc_final: 0.8770 (ppp) REVERT: A 142 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9032 (tp) REVERT: A 270 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6571 (mt-10) REVERT: A 367 PRO cc_start: 0.8881 (OUTLIER) cc_final: 0.8591 (Cg_endo) REVERT: B 43 VAL cc_start: 0.7363 (OUTLIER) cc_final: 0.6903 (m) REVERT: B 50 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8362 (ptpt) REVERT: B 184 ASP cc_start: 0.9055 (m-30) cc_final: 0.8765 (m-30) REVERT: C 82 MET cc_start: 0.9235 (tpt) cc_final: 0.9019 (tpt) REVERT: D 47 MET cc_start: 0.5180 (ptm) cc_final: 0.4940 (ppp) REVERT: D 147 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.9040 (ptp90) REVERT: E 57 GLU cc_start: 0.8621 (tt0) cc_final: 0.8348 (tp30) REVERT: E 59 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8261 (tp-100) REVERT: F 117 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8327 (mp0) REVERT: F 147 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8570 (ptp-170) REVERT: F 269 MET cc_start: 0.9529 (mtm) cc_final: 0.9316 (mtm) REVERT: G 59 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.9190 (tp40) REVERT: G 149 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8331 (m) REVERT: G 292 ASP cc_start: 0.9122 (m-30) cc_final: 0.8877 (t0) REVERT: G 325 MET cc_start: 0.7986 (mmt) cc_final: 0.7783 (mmp) REVERT: G 359 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8761 (tptm) REVERT: T 71 LEU cc_start: 0.8689 (mt) cc_final: 0.8484 (mp) REVERT: T 73 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8451 (pttm) REVERT: T 182 ASP cc_start: 0.8107 (t70) cc_final: 0.7564 (t70) REVERT: T 210 ILE cc_start: 0.8525 (mm) cc_final: 0.8306 (tt) REVERT: T 305 MET cc_start: 0.7912 (mmm) cc_final: 0.7222 (mmm) outliers start: 86 outliers final: 6 residues processed: 392 average time/residue: 0.3943 time to fit residues: 227.4244 Evaluate side-chains 194 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 367 PRO Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain T residue 73 LYS Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 177 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 9.9990 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: 2.9990 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 59 GLN E 115 ASN F 371 HIS G 41 GLN G 59 GLN ** 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: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22871 Z= 0.307 Angle : 0.610 9.598 31027 Z= 0.297 Chirality : 0.045 0.155 3449 Planarity : 0.004 0.056 3975 Dihedral : 9.667 154.829 3217 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.75 % Allowed : 10.44 % Favored : 87.82 % 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: 0.68 (0.16), residues: 1154 sheet: 0.54 (0.23), residues: 496 loop : 0.32 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 356 HIS 0.009 0.001 HIS B 161 PHE 0.016 0.001 PHE C 127 TYR 0.016 0.001 TYR T 87 ARG 0.007 0.001 ARG D 372 *********************** 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 215 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 173 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.4911 (tpp) cc_final: 0.4551 (pmm) REVERT: A 82 MET cc_start: 0.8987 (tpt) cc_final: 0.8483 (tpp) REVERT: A 118 LYS cc_start: 0.9307 (tptt) cc_final: 0.9047 (tppt) REVERT: A 132 MET cc_start: 0.9111 (ppp) cc_final: 0.8851 (ppp) REVERT: A 227 MET cc_start: 0.8595 (tpt) cc_final: 0.8350 (mmm) REVERT: B 50 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7823 (pptt) REVERT: B 119 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8451 (mtm) REVERT: B 176 MET cc_start: 0.8532 (mmm) cc_final: 0.7715 (mtt) REVERT: E 132 MET cc_start: 0.9381 (ppp) cc_final: 0.8794 (ppp) REVERT: F 64 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9181 (pp) REVERT: F 269 MET cc_start: 0.9521 (mtm) cc_final: 0.9280 (mtm) REVERT: G 149 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8532 (m) REVERT: G 292 ASP cc_start: 0.9121 (m-30) cc_final: 0.8884 (t0) REVERT: G 325 MET cc_start: 0.8024 (mmt) cc_final: 0.7711 (mmp) REVERT: T 70 HIS cc_start: 0.6856 (m90) cc_final: 0.6595 (t70) REVERT: T 242 TYR cc_start: 0.7874 (m-80) cc_final: 0.7228 (m-80) REVERT: T 304 SER cc_start: 0.8726 (p) cc_final: 0.8335 (t) outliers start: 42 outliers final: 24 residues processed: 207 average time/residue: 0.3039 time to fit residues: 102.1982 Evaluate side-chains 185 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 238 ASP Chi-restraints excluded: chain T residue 318 HIS Chi-restraints excluded: chain T residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 213 optimal weight: 7.9990 chunk 174 optimal weight: 0.0470 chunk 70 optimal weight: 0.6980 chunk 256 optimal weight: 8.9990 chunk 277 optimal weight: 6.9990 chunk 228 optimal weight: 0.1980 chunk 254 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 49 GLN D 115 ASN E 115 ASN T 318 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22871 Z= 0.133 Angle : 0.528 9.521 31027 Z= 0.250 Chirality : 0.042 0.151 3449 Planarity : 0.004 0.052 3975 Dihedral : 7.755 128.665 3182 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.21 % Allowed : 11.89 % Favored : 86.90 % 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: 0.98 (0.17), residues: 2794 helix: 0.96 (0.16), residues: 1140 sheet: 0.67 (0.22), residues: 506 loop : 0.52 (0.20), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 356 HIS 0.016 0.001 HIS T 318 PHE 0.017 0.001 PHE C 127 TYR 0.011 0.001 TYR T 242 ARG 0.004 0.000 ARG D 372 *********************** 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 191 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 2.980 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5046 (tpp) cc_final: 0.4687 (pmm) REVERT: A 82 MET cc_start: 0.8954 (tpt) cc_final: 0.8377 (tpp) REVERT: A 118 LYS cc_start: 0.9320 (tptt) cc_final: 0.9091 (tppt) REVERT: A 132 MET cc_start: 0.9083 (ppp) cc_final: 0.8828 (ppp) REVERT: B 50 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7892 (ptpt) REVERT: B 119 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8411 (mtm) REVERT: E 123 MET cc_start: 0.9296 (mmt) cc_final: 0.9066 (mmt) REVERT: E 132 MET cc_start: 0.9334 (ppp) cc_final: 0.8775 (ppp) REVERT: F 64 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9172 (pp) REVERT: F 269 MET cc_start: 0.9426 (mtm) cc_final: 0.9200 (mtp) REVERT: G 292 ASP cc_start: 0.9127 (m-30) cc_final: 0.8830 (t0) REVERT: G 325 MET cc_start: 0.7938 (mmt) cc_final: 0.7719 (mmp) REVERT: T 70 HIS cc_start: 0.6822 (m90) cc_final: 0.6526 (t70) REVERT: T 188 GLU cc_start: 0.8935 (tt0) cc_final: 0.8718 (tp30) outliers start: 29 outliers final: 13 residues processed: 188 average time/residue: 0.3096 time to fit residues: 95.6801 Evaluate side-chains 169 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 238 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN D 41 GLN D 49 GLN E 12 ASN E 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22871 Z= 0.182 Angle : 0.534 8.708 31027 Z= 0.250 Chirality : 0.043 0.145 3449 Planarity : 0.004 0.050 3975 Dihedral : 6.298 96.566 3178 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.29 % Allowed : 11.77 % Favored : 86.94 % 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: 1.08 (0.17), residues: 2794 helix: 1.05 (0.16), residues: 1140 sheet: 0.62 (0.22), residues: 516 loop : 0.62 (0.21), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 356 HIS 0.006 0.001 HIS B 161 PHE 0.010 0.001 PHE D 255 TYR 0.013 0.001 TYR T 242 ARG 0.003 0.000 ARG D 372 *********************** 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 189 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 2.807 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5095 (tpp) cc_final: 0.4817 (pmm) REVERT: A 82 MET cc_start: 0.9015 (tpt) cc_final: 0.8469 (tpp) REVERT: A 118 LYS cc_start: 0.9345 (tptt) cc_final: 0.9134 (tppt) REVERT: A 132 MET cc_start: 0.9130 (ppp) cc_final: 0.8874 (ppp) REVERT: B 50 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7908 (ptpt) REVERT: B 59 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8517 (tm-30) REVERT: C 305 MET cc_start: 0.9088 (mmm) cc_final: 0.8599 (mmm) REVERT: E 132 MET cc_start: 0.9351 (ppp) cc_final: 0.8793 (ppp) REVERT: E 283 MET cc_start: 0.9060 (mmm) cc_final: 0.8722 (mmm) REVERT: E 325 MET cc_start: 0.8921 (mmt) cc_final: 0.8570 (mmp) REVERT: F 64 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9235 (pp) REVERT: F 269 MET cc_start: 0.9416 (mtm) cc_final: 0.9190 (mtp) REVERT: G 292 ASP cc_start: 0.9138 (m-30) cc_final: 0.8829 (t0) REVERT: T 333 MET cc_start: 0.7862 (tpp) cc_final: 0.7650 (ttm) outliers start: 31 outliers final: 18 residues processed: 185 average time/residue: 0.3104 time to fit residues: 94.1631 Evaluate side-chains 174 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 238 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 0.0670 chunk 244 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN E 12 ASN ** T 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2626 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= 0.211 Angle : 0.544 9.329 31027 Z= 0.256 Chirality : 0.043 0.144 3449 Planarity : 0.004 0.051 3975 Dihedral : 5.837 78.762 3177 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.50 % Allowed : 11.98 % 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: 1.12 (0.17), residues: 2794 helix: 1.09 (0.16), residues: 1133 sheet: 0.65 (0.22), residues: 518 loop : 0.64 (0.21), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.006 0.001 HIS B 161 PHE 0.010 0.001 PHE D 255 TYR 0.008 0.001 TYR C 306 ARG 0.003 0.000 ARG G 206 *********************** 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 195 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 159 time to evaluate : 2.594 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9046 (tpt) cc_final: 0.8510 (tpp) REVERT: A 118 LYS cc_start: 0.9307 (tptt) cc_final: 0.8993 (tppt) REVERT: A 132 MET cc_start: 0.9126 (ppp) cc_final: 0.8864 (ppp) REVERT: B 50 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7977 (ptpt) REVERT: B 59 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: D 47 MET cc_start: 0.5769 (OUTLIER) cc_final: 0.5400 (ppp) REVERT: F 64 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9182 (pp) REVERT: G 149 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8526 (m) REVERT: G 292 ASP cc_start: 0.9132 (m-30) cc_final: 0.8848 (t0) REVERT: G 325 MET cc_start: 0.8844 (mmp) cc_final: 0.8474 (mmt) REVERT: G 359 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.8968 (tptm) REVERT: T 322 GLN cc_start: 0.8253 (mp10) cc_final: 0.7839 (pt0) outliers start: 36 outliers final: 24 residues processed: 190 average time/residue: 0.3114 time to fit residues: 97.7506 Evaluate side-chains 183 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 238 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 chunk 226 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.0570 chunk 143 optimal weight: 0.7980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN D 59 GLN D 173 HIS E 12 ASN T 204 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22871 Z= 0.177 Angle : 0.534 10.633 31027 Z= 0.248 Chirality : 0.043 0.146 3449 Planarity : 0.003 0.050 3975 Dihedral : 5.584 73.727 3177 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.54 % Allowed : 12.60 % 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: 1.12 (0.17), residues: 2794 helix: 1.06 (0.16), residues: 1144 sheet: 0.59 (0.23), residues: 524 loop : 0.71 (0.21), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.007 0.001 HIS B 161 PHE 0.010 0.001 PHE D 255 TYR 0.012 0.001 TYR T 242 ARG 0.003 0.000 ARG T 340 *********************** 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 191 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 2.721 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9045 (tpt) cc_final: 0.8479 (tpp) REVERT: A 118 LYS cc_start: 0.9308 (tptt) cc_final: 0.8989 (tppt) REVERT: A 132 MET cc_start: 0.9118 (ppp) cc_final: 0.8857 (ppp) REVERT: A 305 MET cc_start: 0.9230 (mmm) cc_final: 0.9028 (mmt) REVERT: B 50 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8028 (ptpt) REVERT: B 59 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: D 47 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5411 (ppp) REVERT: D 224 GLU cc_start: 0.8406 (mp0) cc_final: 0.8185 (mp0) REVERT: E 132 MET cc_start: 0.9313 (ppp) cc_final: 0.8787 (ppp) REVERT: E 283 MET cc_start: 0.9071 (mmm) cc_final: 0.8668 (mmm) REVERT: F 64 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9171 (pp) REVERT: G 149 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8607 (m) REVERT: G 292 ASP cc_start: 0.9122 (m-30) cc_final: 0.8874 (t0) REVERT: G 359 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.8954 (tptm) REVERT: T 305 MET cc_start: 0.7653 (mmm) cc_final: 0.7360 (tpp) REVERT: T 322 GLN cc_start: 0.8227 (mp10) cc_final: 0.7849 (pt0) outliers start: 37 outliers final: 21 residues processed: 185 average time/residue: 0.3215 time to fit residues: 97.4819 Evaluate side-chains 177 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 115 ASN F 115 ASN ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 22871 Z= 0.483 Angle : 0.680 10.917 31027 Z= 0.328 Chirality : 0.048 0.286 3449 Planarity : 0.004 0.048 3975 Dihedral : 6.222 85.152 3177 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.79 % Allowed : 12.52 % Favored : 85.70 % 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 (0.17), residues: 2794 helix: 0.78 (0.16), residues: 1149 sheet: 0.53 (0.23), residues: 499 loop : 0.19 (0.20), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 79 HIS 0.009 0.001 HIS B 161 PHE 0.016 0.002 PHE G 127 TYR 0.012 0.001 TYR G 69 ARG 0.004 0.001 ARG T 343 *********************** 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 196 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9063 (tpt) cc_final: 0.8509 (tpp) REVERT: A 118 LYS cc_start: 0.9331 (tptt) cc_final: 0.9069 (tppt) REVERT: A 123 MET cc_start: 0.8770 (mmp) cc_final: 0.8565 (mmp) REVERT: A 132 MET cc_start: 0.9142 (ppp) cc_final: 0.8855 (ppp) REVERT: B 50 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7809 (pptt) REVERT: B 59 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: B 132 MET cc_start: 0.8793 (ppp) cc_final: 0.8391 (ppp) REVERT: B 176 MET cc_start: 0.8556 (mmm) cc_final: 0.7965 (mtt) REVERT: C 176 MET cc_start: 0.9100 (mmm) cc_final: 0.8819 (mtp) REVERT: E 47 MET cc_start: 0.6947 (ppp) cc_final: 0.6677 (ppp) REVERT: E 325 MET cc_start: 0.9091 (mmt) cc_final: 0.8723 (mmp) REVERT: F 64 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9187 (pp) REVERT: G 149 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.8692 (m) REVERT: G 292 ASP cc_start: 0.9203 (m-30) cc_final: 0.8953 (t0) REVERT: G 359 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9220 (tppt) REVERT: T 322 GLN cc_start: 0.8323 (mp10) cc_final: 0.8099 (pt0) outliers start: 43 outliers final: 31 residues processed: 190 average time/residue: 0.3354 time to fit residues: 102.6920 Evaluate side-chains 182 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain G residue 372 ARG Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 0.0270 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN D 115 ASN E 12 ASN F 115 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22871 Z= 0.149 Angle : 0.540 11.423 31027 Z= 0.252 Chirality : 0.043 0.212 3449 Planarity : 0.003 0.049 3975 Dihedral : 5.568 71.922 3177 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.21 % Allowed : 13.72 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2794 helix: 1.04 (0.16), residues: 1143 sheet: 0.49 (0.23), residues: 523 loop : 0.56 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS T 70 PHE 0.010 0.001 PHE D 255 TYR 0.012 0.001 TYR T 317 ARG 0.005 0.000 ARG B 372 *********************** 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 180 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 2.541 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9054 (tpt) cc_final: 0.8496 (tpp) REVERT: A 118 LYS cc_start: 0.9320 (tptt) cc_final: 0.9000 (tppt) REVERT: A 132 MET cc_start: 0.9094 (ppp) cc_final: 0.8848 (ppp) REVERT: A 227 MET cc_start: 0.8723 (mmm) cc_final: 0.8522 (mmm) REVERT: B 50 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8132 (ptpt) REVERT: B 59 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: B 132 MET cc_start: 0.8757 (ppp) cc_final: 0.8384 (ppp) REVERT: E 132 MET cc_start: 0.9279 (ppp) cc_final: 0.8726 (ppp) REVERT: E 283 MET cc_start: 0.9019 (mmm) cc_final: 0.8596 (mmm) REVERT: F 64 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9187 (pp) REVERT: G 149 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.8628 (m) REVERT: G 292 ASP cc_start: 0.9155 (m-30) cc_final: 0.8831 (t0) REVERT: G 325 MET cc_start: 0.8538 (mmp) cc_final: 0.8133 (mmt) REVERT: T 81 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.4918 (mmp-170) outliers start: 29 outliers final: 11 residues processed: 175 average time/residue: 0.3087 time to fit residues: 88.1214 Evaluate side-chains 163 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain T residue 81 ARG Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 253 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 115 ASN E 12 ASN F 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 22871 Z= 0.373 Angle : 0.630 12.382 31027 Z= 0.298 Chirality : 0.046 0.209 3449 Planarity : 0.004 0.048 3975 Dihedral : 5.873 82.045 3176 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.50 % Allowed : 13.56 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2794 helix: 0.91 (0.16), residues: 1148 sheet: 0.42 (0.23), residues: 509 loop : 0.29 (0.20), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.007 0.001 HIS B 161 PHE 0.013 0.001 PHE G 127 TYR 0.012 0.001 TYR T 242 ARG 0.004 0.000 ARG T 340 *********************** 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 183 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9042 (tpt) cc_final: 0.8466 (tpp) REVERT: A 132 MET cc_start: 0.9126 (ppp) cc_final: 0.8870 (ppp) REVERT: B 50 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7816 (pptt) REVERT: B 59 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: B 132 MET cc_start: 0.8705 (ppp) cc_final: 0.8223 (ppp) REVERT: B 176 MET cc_start: 0.8558 (mmm) cc_final: 0.7942 (mtt) REVERT: D 47 MET cc_start: 0.6145 (ppp) cc_final: 0.5813 (ppp) REVERT: E 47 MET cc_start: 0.6926 (ppp) cc_final: 0.6637 (ppp) REVERT: E 325 MET cc_start: 0.9062 (mmt) cc_final: 0.8722 (mmp) REVERT: F 64 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9212 (pp) REVERT: G 149 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.8741 (m) REVERT: G 292 ASP cc_start: 0.9188 (m-30) cc_final: 0.8940 (t0) REVERT: G 325 MET cc_start: 0.8655 (mmp) cc_final: 0.8307 (mmt) REVERT: G 359 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9226 (tppt) REVERT: T 81 ARG cc_start: 0.5403 (OUTLIER) cc_final: 0.4788 (mmp-170) REVERT: T 320 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8690 (p) outliers start: 36 outliers final: 25 residues processed: 179 average time/residue: 0.3329 time to fit residues: 96.7513 Evaluate side-chains 176 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain G residue 372 ARG Chi-restraints excluded: chain T residue 81 ARG Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Chi-restraints excluded: chain T residue 320 THR Chi-restraints excluded: chain T residue 339 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.5980 chunk 267 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 E 12 ASN F 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3315 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= 0.189 Angle : 0.559 12.463 31027 Z= 0.261 Chirality : 0.044 0.196 3449 Planarity : 0.004 0.049 3975 Dihedral : 5.583 74.197 3176 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.91 % Allowed : 14.18 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2794 helix: 1.00 (0.16), residues: 1141 sheet: 0.47 (0.23), residues: 509 loop : 0.43 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.009 0.001 HIS T 70 PHE 0.010 0.001 PHE D 255 TYR 0.013 0.001 TYR T 317 ARG 0.005 0.000 ARG B 372 ********************** 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 170 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 4.098 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9046 (tpt) cc_final: 0.8452 (tpp) REVERT: A 132 MET cc_start: 0.9104 (ppp) cc_final: 0.8856 (ppp) REVERT: B 50 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8117 (ptpt) REVERT: B 59 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8333 (tm-30) REVERT: B 132 MET cc_start: 0.8714 (ppp) cc_final: 0.8497 (ppp) REVERT: B 176 MET cc_start: 0.8577 (mmm) cc_final: 0.8108 (mtt) REVERT: C 176 MET cc_start: 0.9106 (mmm) cc_final: 0.8830 (mtp) REVERT: D 47 MET cc_start: 0.6129 (ppp) cc_final: 0.5805 (ppp) REVERT: E 47 MET cc_start: 0.6825 (ppp) cc_final: 0.6595 (ppp) REVERT: E 176 MET cc_start: 0.9201 (mmm) cc_final: 0.8894 (mtp) REVERT: E 283 MET cc_start: 0.8942 (mmm) cc_final: 0.8568 (mmm) REVERT: E 325 MET cc_start: 0.8995 (mmt) cc_final: 0.8670 (mmp) REVERT: F 64 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9198 (pp) REVERT: G 149 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.8690 (m) REVERT: G 292 ASP cc_start: 0.9183 (m-30) cc_final: 0.8921 (t0) REVERT: G 325 MET cc_start: 0.8681 (mmp) cc_final: 0.8318 (mmt) REVERT: T 81 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.4764 (mmp-170) outliers start: 22 outliers final: 17 residues processed: 167 average time/residue: 0.3181 time to fit residues: 88.0055 Evaluate side-chains 167 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain T residue 81 ARG Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 4.9990 chunk 238 optimal weight: 0.0030 chunk 68 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 overall best weight: 0.5328 ------------------------------------------------------------------------------- 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** E 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.050266 restraints weight = 69416.527| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.39 r_work: 0.2691 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22871 Z= 0.139 Angle : 0.541 12.357 31027 Z= 0.249 Chirality : 0.043 0.187 3449 Planarity : 0.003 0.050 3975 Dihedral : 5.263 65.455 3176 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.00 % Allowed : 14.26 % Favored : 84.74 % 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: 1.07 (0.17), residues: 2794 helix: 1.14 (0.16), residues: 1140 sheet: 0.56 (0.23), residues: 510 loop : 0.54 (0.21), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE D 255 TYR 0.015 0.001 TYR T 225 ARG 0.005 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4075.00 seconds wall clock time: 75 minutes 30.50 seconds (4530.50 seconds total)