Starting phenix.real_space_refine on Thu Feb 15 09:44:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnh_27572/02_2024/8dnh_27572_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnh_27572/02_2024/8dnh_27572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnh_27572/02_2024/8dnh_27572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnh_27572/02_2024/8dnh_27572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnh_27572/02_2024/8dnh_27572_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnh_27572/02_2024/8dnh_27572_updated.pdb" } resolution = 2.99 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= 0.009 sd= 0.043 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 8 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 7432 2.51 5 N 1980 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} 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: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2921 Unusual residues: {'ACE': 1} Classifications: {'peptide': 374, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 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} Time building chain proxies: 6.51, per 1000 atoms: 0.55 Number of scatterers: 11796 At special positions: 0 Unit cell: (81.081, 104.247, 171.963, 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 88 16.00 P 8 15.00 Mg 4 11.99 O 2284 8.00 N 1980 7.00 C 7432 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: 4.28 Conformation dependent library (CDL) restraints added in 2.4 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 20 sheets defined 41.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 181 through 195 removed outlier: 4.005A pdb=" N THR A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.771A pdb=" N ARG A 255 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 286 through 293 removed outlier: 5.021A pdb=" N LYS A 290 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 291 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 304 Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.553A pdb=" N SER A 337 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL A 338 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 341 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 181 through 195 removed outlier: 4.005A pdb=" N THR B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.772A pdb=" N ARG B 255 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 260 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 286 through 293 removed outlier: 5.022A pdb=" N LYS B 290 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 291 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 304 Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.554A pdb=" N SER B 337 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL B 338 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 341 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 360 through 363 No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 368 through 371 No H-bonds generated for 'chain 'B' and resid 368 through 371' Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 181 through 195 removed outlier: 4.005A pdb=" N THR C 193 " --> pdb=" O MET C 189 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.772A pdb=" N ARG C 255 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 260 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 286 through 293 removed outlier: 5.022A pdb=" N LYS C 290 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 291 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 334 through 346 removed outlier: 3.554A pdb=" N SER C 337 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL C 338 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 341 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 351 No H-bonds generated for 'chain 'C' and resid 349 through 351' Processing helix chain 'C' and resid 358 through 364 Processing helix chain 'C' and resid 368 through 371 No H-bonds generated for 'chain 'C' and resid 368 through 371' Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 78 through 90 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 136 through 144 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 181 through 195 removed outlier: 4.005A pdb=" N THR D 193 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.772A pdb=" N ARG D 255 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 286 through 293 removed outlier: 5.022A pdb=" N LYS D 290 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP D 291 " --> pdb=" O ILE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 308 through 319 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.553A pdb=" N SER D 337 " --> pdb=" O ARG D 334 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL D 338 " --> pdb=" O LYS D 335 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 341 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 351 No H-bonds generated for 'chain 'D' and resid 349 through 351' Processing helix chain 'D' and resid 358 through 364 Processing helix chain 'D' and resid 368 through 371 No H-bonds generated for 'chain 'D' and resid 368 through 371' Processing sheet with id= A, first strand: chain 'A' and resid 7 through 11 removed outlier: 3.687A pdb=" N PHE A 30 " --> pdb=" O CYS A 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.517A pdb=" N ARG A 36 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 102 through 106 removed outlier: 3.538A pdb=" N TYR A 132 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 296 through 299 removed outlier: 6.615A pdb=" N ILE A 150 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N SER A 299 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N MET A 152 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 149 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 164 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 151 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 162 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 175 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.668A pdb=" N LYS A 237 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 7 through 11 removed outlier: 3.688A pdb=" N PHE B 30 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 33 through 37 removed outlier: 3.516A pdb=" N ARG B 36 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 102 through 106 removed outlier: 3.539A pdb=" N TYR B 132 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 296 through 299 removed outlier: 6.615A pdb=" N ILE B 150 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N SER B 299 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET B 152 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 149 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 164 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 151 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 162 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 175 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.668A pdb=" N LYS B 237 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.687A pdb=" N PHE C 30 " --> pdb=" O CYS C 16 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 33 through 37 removed outlier: 3.517A pdb=" N ARG C 36 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 102 through 106 removed outlier: 3.539A pdb=" N TYR C 132 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 296 through 299 removed outlier: 6.615A pdb=" N ILE C 150 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N SER C 299 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET C 152 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C 149 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 164 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 151 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 162 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 175 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.668A pdb=" N LYS C 237 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 7 through 11 removed outlier: 3.687A pdb=" N PHE D 30 " --> pdb=" O CYS D 16 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 33 through 37 removed outlier: 3.518A pdb=" N ARG D 36 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 102 through 106 removed outlier: 3.592A pdb=" N TYR D 132 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 296 through 299 removed outlier: 6.616A pdb=" N ILE D 150 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N SER D 299 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET D 152 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 149 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 164 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 151 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 162 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 175 " --> pdb=" O THR D 161 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.668A pdb=" N LYS D 237 " --> pdb=" O ILE D 249 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1011 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: 3.15 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1976 1.31 - 1.44: 3136 1.44 - 1.56: 6776 1.56 - 1.69: 12 1.69 - 1.81: 152 Bond restraints: 12052 Sorted by residual: bond pdb=" C HIC D 72 " pdb=" O HIC D 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C HIC B 72 " pdb=" O HIC B 72 " ideal model delta sigma weight residual 1.231 1.358 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C HIC C 72 " pdb=" O HIC C 72 " ideal model delta sigma weight residual 1.231 1.357 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C HIC A 72 " pdb=" O HIC A 72 " ideal model delta sigma weight residual 1.231 1.357 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CA SER C 367 " pdb=" CB SER C 367 " ideal model delta sigma weight residual 1.537 1.484 0.053 1.38e-02 5.25e+03 1.46e+01 ... (remaining 12047 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.66: 339 105.66 - 113.26: 6468 113.26 - 120.86: 5818 120.86 - 128.47: 3647 128.47 - 136.07: 80 Bond angle restraints: 16352 Sorted by residual: angle pdb=" N PRO B 242 " pdb=" CA PRO B 242 " pdb=" C PRO B 242 " ideal model delta sigma weight residual 113.84 122.51 -8.67 1.30e+00 5.92e-01 4.44e+01 angle pdb=" C PRO A 366 " pdb=" CA PRO A 366 " pdb=" CB PRO A 366 " ideal model delta sigma weight residual 112.89 105.66 7.23 1.31e+00 5.83e-01 3.05e+01 angle pdb=" C PRO C 366 " pdb=" CA PRO C 366 " pdb=" CB PRO C 366 " ideal model delta sigma weight residual 112.89 105.67 7.22 1.31e+00 5.83e-01 3.04e+01 angle pdb=" C PRO D 366 " pdb=" CA PRO D 366 " pdb=" CB PRO D 366 " ideal model delta sigma weight residual 112.89 105.69 7.20 1.31e+00 5.83e-01 3.02e+01 angle pdb=" N ASP B 362 " pdb=" CA ASP B 362 " pdb=" C ASP B 362 " ideal model delta sigma weight residual 114.12 107.29 6.83 1.39e+00 5.18e-01 2.41e+01 ... (remaining 16347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.88: 6949 31.88 - 63.76: 274 63.76 - 95.65: 17 95.65 - 127.53: 0 127.53 - 159.41: 12 Dihedral angle restraints: 7252 sinusoidal: 2932 harmonic: 4320 Sorted by residual: dihedral pdb=" CH3 ACE C 0 " pdb=" C ACE C 0 " pdb=" N ASP C 1 " pdb=" CA ASP C 1 " ideal model delta sinusoidal sigma weight residual -180.00 -133.06 -46.94 1 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CH3 ACE B 0 " pdb=" C ACE B 0 " pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sinusoidal sigma weight residual -180.00 -133.07 -46.93 1 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CH3 ACE D 0 " pdb=" C ACE D 0 " pdb=" N ASP D 1 " pdb=" CA ASP D 1 " ideal model delta sinusoidal sigma weight residual -180.00 -133.07 -46.93 1 5.00e+00 4.00e-02 1.22e+02 ... (remaining 7249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1576 0.085 - 0.170: 216 0.170 - 0.255: 19 0.255 - 0.340: 0 0.340 - 0.425: 1 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA PRO B 242 " pdb=" N PRO B 242 " pdb=" C PRO B 242 " pdb=" CB PRO B 242 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA GLU B 240 " pdb=" N GLU B 240 " pdb=" C GLU B 240 " pdb=" CB GLU B 240 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE C 368 " pdb=" N ILE C 368 " pdb=" C ILE C 368 " pdb=" CB ILE C 368 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1809 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE B 0 " -0.075 2.00e-02 2.50e+03 2.28e-01 6.51e+02 pdb=" O ACE B 0 " -0.002 2.00e-02 2.50e+03 pdb=" CH3 ACE B 0 " 0.187 2.00e-02 2.50e+03 pdb=" N ASP B 1 " -0.382 2.00e-02 2.50e+03 pdb=" CA ASP B 1 " 0.272 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 0 " -0.074 2.00e-02 2.50e+03 2.28e-01 6.51e+02 pdb=" O ACE D 0 " -0.003 2.00e-02 2.50e+03 pdb=" CH3 ACE D 0 " 0.187 2.00e-02 2.50e+03 pdb=" N ASP D 1 " -0.382 2.00e-02 2.50e+03 pdb=" CA ASP D 1 " 0.272 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE C 0 " -0.074 2.00e-02 2.50e+03 2.28e-01 6.51e+02 pdb=" O ACE C 0 " -0.002 2.00e-02 2.50e+03 pdb=" CH3 ACE C 0 " 0.187 2.00e-02 2.50e+03 pdb=" N ASP C 1 " -0.382 2.00e-02 2.50e+03 pdb=" CA ASP C 1 " 0.272 2.00e-02 2.50e+03 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 312 2.70 - 3.25: 10790 3.25 - 3.80: 16727 3.80 - 4.35: 21603 4.35 - 4.90: 37533 Nonbonded interactions: 86965 Sorted by model distance: nonbonded pdb=" O ASP D 243 " pdb=" OD1 ASP D 243 " model vdw 2.150 3.040 nonbonded pdb=" O SER B 32 " pdb=" OG SER B 32 " model vdw 2.333 2.440 nonbonded pdb=" O SER D 32 " pdb=" OG SER D 32 " model vdw 2.333 2.440 nonbonded pdb=" O SER C 32 " pdb=" OG SER C 32 " model vdw 2.334 2.440 nonbonded pdb=" O SER A 32 " pdb=" OG SER A 32 " model vdw 2.334 2.440 ... (remaining 86960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.320 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.300 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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 : 0.006 0.127 12052 Z= 0.389 Angle : 0.875 8.665 16352 Z= 0.534 Chirality : 0.058 0.425 1812 Planarity : 0.011 0.228 2096 Dihedral : 17.003 159.410 4484 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.16 % Allowed : 11.39 % Favored : 88.45 % 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: 0.38 (0.22), residues: 1476 helix: 0.70 (0.22), residues: 584 sheet: 0.56 (0.36), residues: 220 loop : -0.13 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 78 HIS 0.004 0.001 HIS A 172 PHE 0.013 0.001 PHE A 89 TYR 0.012 0.001 TYR B 336 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 1.178 Fit side-chains REVERT: A 43 MET cc_start: 0.4364 (mmp) cc_final: 0.3568 (mtm) REVERT: A 67 LYS cc_start: 0.7200 (mttm) cc_final: 0.6879 (ptpt) REVERT: A 190 LYS cc_start: 0.6942 (ttmt) cc_final: 0.6206 (mttt) REVERT: A 240 GLU cc_start: 0.6330 (mt-10) cc_final: 0.5319 (pm20) REVERT: A 270 SER cc_start: 0.7023 (t) cc_final: 0.6822 (t) REVERT: A 287 ASP cc_start: 0.6812 (t70) cc_final: 0.6322 (t70) REVERT: A 295 ASN cc_start: 0.7701 (m-40) cc_final: 0.7381 (m-40) REVERT: A 312 MET cc_start: 0.8364 (tpp) cc_final: 0.8134 (tpt) REVERT: A 327 LYS cc_start: 0.6915 (mttp) cc_final: 0.6439 (pttt) REVERT: A 344 ILE cc_start: 0.6118 (mt) cc_final: 0.5896 (mp) REVERT: A 369 VAL cc_start: 0.7060 (t) cc_final: 0.6779 (p) REVERT: B 46 MET cc_start: 0.2908 (mmm) cc_final: 0.2389 (tmm) REVERT: B 49 LYS cc_start: 0.7633 (mtpp) cc_final: 0.6842 (mptt) REVERT: B 94 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6796 (mtm110) REVERT: B 116 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6418 (mt-10) REVERT: B 124 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6420 (OUTLIER) REVERT: B 205 ARG cc_start: 0.6808 (ttm170) cc_final: 0.6606 (ttp80) REVERT: B 222 PHE cc_start: 0.7782 (t80) cc_final: 0.7462 (t80) REVERT: B 223 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6347 (mm-30) REVERT: B 271 CYS cc_start: 0.8531 (m) cc_final: 0.7548 (m) REVERT: B 273 ILE cc_start: 0.7402 (mm) cc_final: 0.7123 (tt) REVERT: B 282 MET cc_start: 0.8177 (mmt) cc_final: 0.7935 (mmm) REVERT: B 304 MET cc_start: 0.8336 (tpt) cc_final: 0.7958 (tpt) REVERT: B 327 LYS cc_start: 0.7823 (mttp) cc_final: 0.7365 (mttt) REVERT: B 357 SER cc_start: 0.7630 (m) cc_final: 0.7155 (p) REVERT: C 49 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7307 (mttm) REVERT: C 81 MET cc_start: 0.7446 (tpp) cc_final: 0.7211 (mmm) REVERT: C 210 ASP cc_start: 0.6871 (m-30) cc_final: 0.6446 (t0) REVERT: C 273 ILE cc_start: 0.8037 (mm) cc_final: 0.7557 (pt) REVERT: C 275 GLU cc_start: 0.6836 (tp30) cc_final: 0.6399 (tt0) REVERT: C 285 ASP cc_start: 0.6803 (m-30) cc_final: 0.6599 (m-30) REVERT: C 290 LYS cc_start: 0.7464 (tttm) cc_final: 0.7167 (ttpt) REVERT: C 327 LYS cc_start: 0.6742 (mttp) cc_final: 0.6215 (mppt) REVERT: C 358 LYS cc_start: 0.7353 (tmtt) cc_final: 0.6818 (tppt) REVERT: C 362 ASP cc_start: 0.6510 (t0) cc_final: 0.5635 (m-30) REVERT: D 46 MET cc_start: 0.3668 (mmm) cc_final: 0.3443 (ttm) REVERT: D 49 LYS cc_start: 0.6576 (mtpp) cc_final: 0.5763 (tppt) REVERT: D 50 ASP cc_start: 0.5947 (m-30) cc_final: 0.5337 (p0) REVERT: D 59 SER cc_start: 0.7534 (t) cc_final: 0.7316 (m) REVERT: D 90 TYR cc_start: 0.8162 (m-80) cc_final: 0.7935 (m-80) REVERT: D 124 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6458 (pt0) REVERT: D 132 TYR cc_start: 0.8351 (t80) cc_final: 0.7911 (t80) REVERT: D 166 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6274 (mt-10) REVERT: D 191 ILE cc_start: 0.7295 (tt) cc_final: 0.6969 (pt) REVERT: D 206 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7468 (mm-30) REVERT: D 210 ASP cc_start: 0.7139 (m-30) cc_final: 0.6645 (m-30) REVERT: D 237 LYS cc_start: 0.7988 (mmtt) cc_final: 0.7528 (mttt) REVERT: D 315 GLU cc_start: 0.6454 (mm-30) cc_final: 0.6165 (mt-10) REVERT: D 352 GLN cc_start: 0.7141 (mm110) cc_final: 0.6779 (mm110) outliers start: 2 outliers final: 2 residues processed: 266 average time/residue: 1.1879 time to fit residues: 341.7309 Evaluate side-chains 161 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 0.0000 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN C 100 HIS D 11 ASN D 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12052 Z= 0.305 Angle : 0.667 6.460 16352 Z= 0.339 Chirality : 0.048 0.143 1812 Planarity : 0.005 0.053 2096 Dihedral : 13.531 178.873 1686 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.01 % Allowed : 17.56 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1476 helix: 0.15 (0.21), residues: 576 sheet: 0.46 (0.32), residues: 260 loop : -0.41 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 85 HIS 0.007 0.002 HIS B 100 PHE 0.016 0.002 PHE A 20 TYR 0.017 0.002 TYR C 142 ARG 0.006 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 1.311 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4064 (mmp) cc_final: 0.2941 (mtm) REVERT: A 83 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6839 (mppt) REVERT: A 183 ASP cc_start: 0.7012 (m-30) cc_final: 0.6732 (m-30) REVERT: A 190 LYS cc_start: 0.7292 (ttmt) cc_final: 0.6471 (mttt) REVERT: A 240 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5907 (tt0) REVERT: A 271 CYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6570 (p) REVERT: A 275 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6440 (mm-30) REVERT: A 287 ASP cc_start: 0.6940 (t70) cc_final: 0.6607 (t70) REVERT: A 312 MET cc_start: 0.8189 (tpp) cc_final: 0.7961 (tpt) REVERT: A 327 LYS cc_start: 0.6954 (mttp) cc_final: 0.6474 (pttt) REVERT: A 344 ILE cc_start: 0.5801 (mt) cc_final: 0.5589 (mp) REVERT: A 369 VAL cc_start: 0.7050 (t) cc_final: 0.6788 (p) REVERT: B 46 MET cc_start: 0.2757 (mmm) cc_final: 0.2107 (tmm) REVERT: B 49 LYS cc_start: 0.7528 (mtpp) cc_final: 0.6564 (mppt) REVERT: B 67 LYS cc_start: 0.7334 (mttm) cc_final: 0.6846 (mtmm) REVERT: B 90 TYR cc_start: 0.7807 (m-80) cc_final: 0.7355 (m-80) REVERT: B 94 ARG cc_start: 0.7478 (mtt180) cc_final: 0.6860 (mtm110) REVERT: B 116 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6252 (mt-10) REVERT: B 124 GLU cc_start: 0.6421 (mt-10) cc_final: 0.5951 (pt0) REVERT: B 182 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6644 (mtt90) REVERT: B 271 CYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7822 (p) REVERT: B 304 MET cc_start: 0.8239 (tpt) cc_final: 0.7760 (tpt) REVERT: B 327 LYS cc_start: 0.7806 (mttp) cc_final: 0.7332 (mttt) REVERT: B 357 SER cc_start: 0.8046 (m) cc_final: 0.7602 (t) REVERT: B 360 GLU cc_start: 0.6335 (mt-10) cc_final: 0.6057 (mt-10) REVERT: C 46 MET cc_start: 0.4678 (OUTLIER) cc_final: 0.4307 (tpp) REVERT: C 49 LYS cc_start: 0.7740 (mtpp) cc_final: 0.7458 (mttm) REVERT: C 50 ASP cc_start: 0.6858 (m-30) cc_final: 0.6402 (p0) REVERT: C 81 MET cc_start: 0.7365 (tpp) cc_final: 0.7161 (mmm) REVERT: C 94 ARG cc_start: 0.7444 (mmm160) cc_final: 0.7102 (mtm-85) REVERT: C 124 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5910 (mt-10) REVERT: C 190 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7523 (ttmm) REVERT: C 237 LYS cc_start: 0.6287 (OUTLIER) cc_final: 0.6011 (mttt) REVERT: C 275 GLU cc_start: 0.6874 (tp30) cc_final: 0.6510 (tt0) REVERT: C 327 LYS cc_start: 0.7044 (mttp) cc_final: 0.6534 (mppt) REVERT: C 362 ASP cc_start: 0.6507 (t0) cc_final: 0.5432 (m-30) REVERT: D 49 LYS cc_start: 0.6832 (mtpp) cc_final: 0.6221 (mmtm) REVERT: D 50 ASP cc_start: 0.6491 (m-30) cc_final: 0.6012 (p0) REVERT: D 56 GLU cc_start: 0.6950 (tp30) cc_final: 0.6682 (tp30) REVERT: D 59 SER cc_start: 0.7497 (t) cc_final: 0.7250 (m) REVERT: D 82 GLU cc_start: 0.6698 (pp20) cc_final: 0.6329 (pp20) REVERT: D 92 GLU cc_start: 0.6273 (tp30) cc_final: 0.5575 (mt-10) REVERT: D 98 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: D 124 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6430 (pt0) REVERT: D 131 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7749 (ttt) REVERT: D 146 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7489 (ptp-110) REVERT: D 152 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7194 (tpt) REVERT: D 271 CYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7379 (p) REVERT: D 297 VAL cc_start: 0.7997 (t) cc_final: 0.7778 (m) REVERT: D 315 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6155 (mt-10) REVERT: D 352 GLN cc_start: 0.7196 (mm110) cc_final: 0.6817 (mm110) outliers start: 38 outliers final: 12 residues processed: 201 average time/residue: 1.2699 time to fit residues: 275.6496 Evaluate side-chains 171 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 347 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.0370 chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 120 GLN B 262 GLN C 100 HIS D 11 ASN D 100 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12052 Z= 0.206 Angle : 0.566 6.541 16352 Z= 0.275 Chirality : 0.044 0.131 1812 Planarity : 0.004 0.056 2096 Dihedral : 11.883 174.187 1686 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.51 % Allowed : 18.83 % Favored : 76.66 % 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: -0.15 (0.21), residues: 1476 helix: 0.25 (0.21), residues: 600 sheet: 0.31 (0.31), residues: 280 loop : -0.51 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 78 HIS 0.007 0.001 HIS D 100 PHE 0.016 0.001 PHE B 222 TYR 0.013 0.001 TYR C 239 ARG 0.004 0.000 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 153 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4045 (mmp) cc_final: 0.2918 (mtm) REVERT: A 183 ASP cc_start: 0.7052 (m-30) cc_final: 0.6781 (m-30) REVERT: A 190 LYS cc_start: 0.7310 (ttmt) cc_final: 0.6421 (mttt) REVERT: A 240 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5884 (tt0) REVERT: A 271 CYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6750 (p) REVERT: A 275 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6374 (mm-30) REVERT: A 287 ASP cc_start: 0.7044 (t70) cc_final: 0.6712 (t70) REVERT: A 312 MET cc_start: 0.8268 (tpp) cc_final: 0.8045 (tpt) REVERT: A 327 LYS cc_start: 0.6986 (mttp) cc_final: 0.6462 (pttt) REVERT: A 369 VAL cc_start: 0.6870 (t) cc_final: 0.6629 (p) REVERT: B 15 MET cc_start: 0.7764 (mmm) cc_final: 0.7476 (mmm) REVERT: B 46 MET cc_start: 0.2750 (mmm) cc_final: 0.2121 (tmm) REVERT: B 49 LYS cc_start: 0.7497 (mtpp) cc_final: 0.6508 (mppt) REVERT: B 67 LYS cc_start: 0.7507 (mttm) cc_final: 0.6976 (mtmm) REVERT: B 81 MET cc_start: 0.6892 (tpt) cc_final: 0.6543 (tpp) REVERT: B 90 TYR cc_start: 0.7740 (m-80) cc_final: 0.7270 (m-80) REVERT: B 94 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6845 (mtm110) REVERT: B 116 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6261 (mt-10) REVERT: B 124 GLU cc_start: 0.6341 (mt-10) cc_final: 0.5829 (pt0) REVERT: B 166 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: B 271 CYS cc_start: 0.8307 (m) cc_final: 0.7701 (p) REVERT: B 282 MET cc_start: 0.8190 (tpp) cc_final: 0.7905 (mmp) REVERT: B 327 LYS cc_start: 0.7746 (mttp) cc_final: 0.7269 (mttt) REVERT: B 357 SER cc_start: 0.7929 (m) cc_final: 0.7524 (t) REVERT: B 366 PRO cc_start: 0.7513 (Cg_endo) cc_final: 0.7160 (Cg_exo) REVERT: C 46 MET cc_start: 0.4855 (OUTLIER) cc_final: 0.4492 (tpp) REVERT: C 49 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7487 (mttm) REVERT: C 94 ARG cc_start: 0.7351 (mmm160) cc_final: 0.6993 (mtm-85) REVERT: C 124 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5947 (mt-10) REVERT: C 237 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.6130 (mttt) REVERT: C 271 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7713 (p) REVERT: C 275 GLU cc_start: 0.7081 (tp30) cc_final: 0.6711 (tt0) REVERT: C 327 LYS cc_start: 0.7155 (mttp) cc_final: 0.6533 (mtmt) REVERT: C 357 SER cc_start: 0.7742 (m) cc_final: 0.7416 (t) REVERT: C 362 ASP cc_start: 0.6772 (t0) cc_final: 0.5719 (m-30) REVERT: D 49 LYS cc_start: 0.6936 (mtpp) cc_final: 0.6381 (mmtm) REVERT: D 50 ASP cc_start: 0.6654 (m-30) cc_final: 0.6141 (p0) REVERT: D 56 GLU cc_start: 0.6864 (tp30) cc_final: 0.6529 (tp30) REVERT: D 59 SER cc_start: 0.7522 (OUTLIER) cc_final: 0.7301 (m) REVERT: D 82 GLU cc_start: 0.6693 (pp20) cc_final: 0.6278 (pp20) REVERT: D 92 GLU cc_start: 0.6427 (tp30) cc_final: 0.5845 (mm-30) REVERT: D 98 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: D 124 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6356 (pt0) REVERT: D 152 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7033 (tpt) REVERT: D 315 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6329 (mm-30) REVERT: D 352 GLN cc_start: 0.7146 (mm110) cc_final: 0.6801 (mm110) REVERT: D 362 ASP cc_start: 0.6068 (t0) cc_final: 0.5460 (m-30) outliers start: 57 outliers final: 22 residues processed: 187 average time/residue: 1.2626 time to fit residues: 255.7446 Evaluate side-chains 173 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 369 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN D 11 ASN D 370 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12052 Z= 0.412 Angle : 0.696 7.089 16352 Z= 0.353 Chirality : 0.050 0.159 1812 Planarity : 0.006 0.061 2096 Dihedral : 11.798 161.743 1686 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.93 % Allowed : 19.46 % Favored : 74.60 % 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: -0.91 (0.21), residues: 1476 helix: -0.19 (0.21), residues: 600 sheet: -0.16 (0.30), residues: 288 loop : -1.13 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 355 HIS 0.007 0.002 HIS C 100 PHE 0.018 0.002 PHE C 265 TYR 0.019 0.002 TYR B 336 ARG 0.004 0.001 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 150 time to evaluate : 1.265 Fit side-chains REVERT: A 43 MET cc_start: 0.4143 (mmp) cc_final: 0.2756 (mtm) REVERT: A 46 MET cc_start: 0.2403 (ttt) cc_final: 0.2177 (tpt) REVERT: A 49 LYS cc_start: 0.5524 (mtpp) cc_final: 0.5117 (ptmt) REVERT: A 147 THR cc_start: 0.8213 (p) cc_final: 0.7908 (m) REVERT: A 183 ASP cc_start: 0.7126 (m-30) cc_final: 0.6826 (m-30) REVERT: A 190 LYS cc_start: 0.7311 (ttmt) cc_final: 0.6338 (mttt) REVERT: A 240 GLU cc_start: 0.6391 (mt-10) cc_final: 0.5898 (tt0) REVERT: A 271 CYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6944 (p) REVERT: A 275 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6472 (mm-30) REVERT: A 287 ASP cc_start: 0.7301 (t70) cc_final: 0.6865 (t70) REVERT: A 312 MET cc_start: 0.8328 (tpp) cc_final: 0.8086 (tpt) REVERT: A 327 LYS cc_start: 0.6858 (mttp) cc_final: 0.6596 (mptp) REVERT: A 369 VAL cc_start: 0.6815 (t) cc_final: 0.6525 (p) REVERT: B 15 MET cc_start: 0.8079 (mmm) cc_final: 0.7693 (mtt) REVERT: B 46 MET cc_start: 0.2714 (mmm) cc_final: 0.1990 (tmm) REVERT: B 49 LYS cc_start: 0.7526 (mtpp) cc_final: 0.6563 (mppt) REVERT: B 67 LYS cc_start: 0.7413 (mttm) cc_final: 0.6851 (mtmm) REVERT: B 81 MET cc_start: 0.7116 (tpt) cc_final: 0.6767 (tpp) REVERT: B 90 TYR cc_start: 0.7848 (m-80) cc_final: 0.7363 (m-80) REVERT: B 94 ARG cc_start: 0.7411 (mtt180) cc_final: 0.6727 (mtm110) REVERT: B 116 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6281 (mt-10) REVERT: B 124 GLU cc_start: 0.5933 (mt-10) cc_final: 0.5418 (pt0) REVERT: B 215 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6878 (mp) REVERT: B 271 CYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7542 (p) REVERT: B 327 LYS cc_start: 0.7583 (mttp) cc_final: 0.7142 (mttt) REVERT: B 362 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.5953 (m-30) REVERT: B 366 PRO cc_start: 0.7568 (Cg_endo) cc_final: 0.7328 (Cg_exo) REVERT: C 46 MET cc_start: 0.5111 (OUTLIER) cc_final: 0.4690 (tpp) REVERT: C 49 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7639 (mttm) REVERT: C 50 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6526 (p0) REVERT: C 94 ARG cc_start: 0.7382 (mmm160) cc_final: 0.6978 (mtm110) REVERT: C 124 GLU cc_start: 0.6266 (mt-10) cc_final: 0.5621 (mt-10) REVERT: C 275 GLU cc_start: 0.7151 (tp30) cc_final: 0.6793 (tt0) REVERT: C 327 LYS cc_start: 0.7158 (mttp) cc_final: 0.6584 (mppt) REVERT: C 357 SER cc_start: 0.8064 (m) cc_final: 0.7831 (t) REVERT: C 362 ASP cc_start: 0.6883 (t0) cc_final: 0.5811 (m-30) REVERT: D 49 LYS cc_start: 0.6912 (mtpp) cc_final: 0.6286 (mmtm) REVERT: D 50 ASP cc_start: 0.6886 (m-30) cc_final: 0.6471 (p0) REVERT: D 56 GLU cc_start: 0.6971 (tp30) cc_final: 0.6655 (tp30) REVERT: D 82 GLU cc_start: 0.6654 (pp20) cc_final: 0.6209 (pp20) REVERT: D 92 GLU cc_start: 0.6552 (tp30) cc_final: 0.5929 (mm-30) REVERT: D 98 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: D 124 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6216 (pt0) REVERT: D 152 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7480 (tpt) REVERT: D 221 ASP cc_start: 0.5152 (p0) cc_final: 0.4846 (p0) REVERT: D 271 CYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7488 (p) REVERT: D 315 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6255 (mp0) REVERT: D 352 GLN cc_start: 0.7261 (mm110) cc_final: 0.6918 (mm110) REVERT: D 362 ASP cc_start: 0.6278 (t0) cc_final: 0.5692 (p0) outliers start: 75 outliers final: 38 residues processed: 202 average time/residue: 1.1845 time to fit residues: 259.8156 Evaluate side-chains 190 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 312 MET Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 369 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 114 ASN C 160 HIS D 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12052 Z= 0.167 Angle : 0.543 6.609 16352 Z= 0.263 Chirality : 0.043 0.129 1812 Planarity : 0.005 0.059 2096 Dihedral : 11.040 156.307 1686 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.64 % Allowed : 22.39 % Favored : 73.97 % 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: -0.62 (0.21), residues: 1476 helix: -0.05 (0.21), residues: 604 sheet: -0.02 (0.29), residues: 296 loop : -0.85 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 78 HIS 0.003 0.001 HIS B 100 PHE 0.008 0.001 PHE B 222 TYR 0.012 0.001 TYR A 239 ARG 0.006 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 145 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4401 (mmp) cc_final: 0.2745 (mtm) REVERT: A 46 MET cc_start: 0.2076 (ttt) cc_final: 0.1820 (tpt) REVERT: A 49 LYS cc_start: 0.5446 (mtpp) cc_final: 0.5122 (ptmt) REVERT: A 147 THR cc_start: 0.8153 (p) cc_final: 0.7896 (m) REVERT: A 183 ASP cc_start: 0.7018 (m-30) cc_final: 0.6730 (m-30) REVERT: A 190 LYS cc_start: 0.7203 (ttmt) cc_final: 0.6274 (mttt) REVERT: A 240 GLU cc_start: 0.6184 (mt-10) cc_final: 0.5870 (tt0) REVERT: A 271 CYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7025 (p) REVERT: A 275 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6505 (mm-30) REVERT: A 287 ASP cc_start: 0.7188 (t70) cc_final: 0.6789 (t70) REVERT: A 312 MET cc_start: 0.8209 (tpp) cc_final: 0.7947 (tpt) REVERT: A 313 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: A 327 LYS cc_start: 0.6819 (mttp) cc_final: 0.6565 (mptp) REVERT: A 369 VAL cc_start: 0.6759 (t) cc_final: 0.6480 (p) REVERT: B 46 MET cc_start: 0.2681 (mmm) cc_final: 0.1963 (tmm) REVERT: B 49 LYS cc_start: 0.7481 (mtpp) cc_final: 0.6541 (mppt) REVERT: B 67 LYS cc_start: 0.7499 (mttm) cc_final: 0.6917 (mtmm) REVERT: B 81 MET cc_start: 0.6959 (tpt) cc_final: 0.6689 (tpp) REVERT: B 90 TYR cc_start: 0.7759 (m-80) cc_final: 0.7245 (m-80) REVERT: B 94 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6778 (mtm110) REVERT: B 116 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6151 (mt-10) REVERT: B 124 GLU cc_start: 0.6041 (mt-10) cc_final: 0.5419 (pt0) REVERT: B 147 THR cc_start: 0.8687 (p) cc_final: 0.8213 (t) REVERT: B 271 CYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7568 (p) REVERT: B 327 LYS cc_start: 0.7551 (mttp) cc_final: 0.7109 (mttt) REVERT: B 357 SER cc_start: 0.7868 (m) cc_final: 0.7544 (t) REVERT: C 46 MET cc_start: 0.5001 (OUTLIER) cc_final: 0.4567 (tpp) REVERT: C 49 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7601 (mttm) REVERT: C 94 ARG cc_start: 0.7409 (mmm160) cc_final: 0.7038 (mtm110) REVERT: C 275 GLU cc_start: 0.7131 (tp30) cc_final: 0.6774 (tt0) REVERT: C 327 LYS cc_start: 0.7131 (mttp) cc_final: 0.6485 (mtmt) REVERT: C 357 SER cc_start: 0.7891 (m) cc_final: 0.7662 (t) REVERT: C 362 ASP cc_start: 0.6876 (t0) cc_final: 0.5796 (m-30) REVERT: D 49 LYS cc_start: 0.6872 (mtpp) cc_final: 0.6304 (mmtm) REVERT: D 50 ASP cc_start: 0.6832 (m-30) cc_final: 0.6474 (p0) REVERT: D 82 GLU cc_start: 0.6657 (pp20) cc_final: 0.6311 (pp20) REVERT: D 124 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6256 (pt0) REVERT: D 131 MET cc_start: 0.7961 (ttt) cc_final: 0.7529 (tpt) REVERT: D 152 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7553 (tpt) REVERT: D 271 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7475 (p) REVERT: D 315 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6188 (mm-30) REVERT: D 352 GLN cc_start: 0.7265 (mm110) cc_final: 0.6908 (mm110) REVERT: D 362 ASP cc_start: 0.6239 (t0) cc_final: 0.5622 (p0) outliers start: 46 outliers final: 17 residues processed: 175 average time/residue: 1.2198 time to fit residues: 231.3761 Evaluate side-chains 164 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 287 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 0.2980 chunk 118 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 120 GLN D 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12052 Z= 0.304 Angle : 0.614 8.153 16352 Z= 0.303 Chirality : 0.046 0.138 1812 Planarity : 0.005 0.059 2096 Dihedral : 11.111 155.908 1684 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.83 % Allowed : 21.91 % Favored : 73.26 % 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: -0.60 (0.21), residues: 1476 helix: 0.10 (0.22), residues: 576 sheet: -0.02 (0.29), residues: 288 loop : -0.95 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 355 HIS 0.004 0.001 HIS B 100 PHE 0.011 0.002 PHE C 265 TYR 0.016 0.002 TYR C 142 ARG 0.007 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 141 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4528 (mmp) cc_final: 0.2929 (mtm) REVERT: A 46 MET cc_start: 0.2073 (OUTLIER) cc_final: 0.1835 (tpt) REVERT: A 49 LYS cc_start: 0.5521 (mtpp) cc_final: 0.5133 (ptmt) REVERT: A 147 THR cc_start: 0.8231 (p) cc_final: 0.7968 (m) REVERT: A 183 ASP cc_start: 0.7089 (m-30) cc_final: 0.6795 (m-30) REVERT: A 190 LYS cc_start: 0.7242 (ttmt) cc_final: 0.6330 (mttt) REVERT: A 240 GLU cc_start: 0.6319 (mt-10) cc_final: 0.5862 (tt0) REVERT: A 271 CYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7086 (p) REVERT: A 275 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6523 (mm-30) REVERT: A 287 ASP cc_start: 0.7266 (t70) cc_final: 0.6877 (t70) REVERT: A 312 MET cc_start: 0.8314 (tpp) cc_final: 0.8058 (tpt) REVERT: A 327 LYS cc_start: 0.6704 (mttp) cc_final: 0.6364 (mptp) REVERT: B 15 MET cc_start: 0.8017 (mmm) cc_final: 0.7654 (mtt) REVERT: B 46 MET cc_start: 0.2835 (mmm) cc_final: 0.2228 (tmm) REVERT: B 49 LYS cc_start: 0.7471 (mtpp) cc_final: 0.6540 (mppt) REVERT: B 67 LYS cc_start: 0.7548 (mttm) cc_final: 0.6946 (mtmm) REVERT: B 81 MET cc_start: 0.7115 (tpt) cc_final: 0.6834 (tpp) REVERT: B 90 TYR cc_start: 0.7843 (m-80) cc_final: 0.7369 (m-80) REVERT: B 94 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6484 (mtm110) REVERT: B 116 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6227 (mt-10) REVERT: B 124 GLU cc_start: 0.6057 (mt-10) cc_final: 0.5479 (pt0) REVERT: B 182 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6746 (ttm170) REVERT: B 271 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7555 (p) REVERT: B 327 LYS cc_start: 0.7527 (mttp) cc_final: 0.7106 (mttt) REVERT: C 46 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.4646 (tpp) REVERT: C 49 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7619 (mttm) REVERT: C 94 ARG cc_start: 0.7399 (mmm160) cc_final: 0.6970 (mtm110) REVERT: C 275 GLU cc_start: 0.7136 (tp30) cc_final: 0.6747 (tt0) REVERT: C 327 LYS cc_start: 0.7148 (mttp) cc_final: 0.6748 (mtmp) REVERT: C 357 SER cc_start: 0.8027 (m) cc_final: 0.7824 (t) REVERT: C 362 ASP cc_start: 0.6868 (t0) cc_final: 0.5800 (m-30) REVERT: D 49 LYS cc_start: 0.6906 (mtpp) cc_final: 0.6369 (mmtm) REVERT: D 50 ASP cc_start: 0.6942 (m-30) cc_final: 0.6564 (p0) REVERT: D 56 GLU cc_start: 0.6950 (tp30) cc_final: 0.6574 (tp30) REVERT: D 82 GLU cc_start: 0.6707 (pp20) cc_final: 0.6303 (pp20) REVERT: D 98 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6268 (mp0) REVERT: D 124 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6201 (pt0) REVERT: D 152 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7526 (tpt) REVERT: D 162 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7882 (p) REVERT: D 271 CYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7478 (p) REVERT: D 315 GLU cc_start: 0.6580 (mm-30) cc_final: 0.5996 (mt-10) REVERT: D 352 GLN cc_start: 0.7382 (mm110) cc_final: 0.7048 (mm110) REVERT: D 362 ASP cc_start: 0.6271 (t0) cc_final: 0.5555 (p0) outliers start: 61 outliers final: 29 residues processed: 184 average time/residue: 1.2465 time to fit residues: 248.5674 Evaluate side-chains 177 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 347 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.0970 chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN D 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12052 Z= 0.295 Angle : 0.603 8.761 16352 Z= 0.298 Chirality : 0.045 0.137 1812 Planarity : 0.005 0.063 2096 Dihedral : 11.024 153.379 1684 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.19 % Allowed : 22.55 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1476 helix: 0.07 (0.22), residues: 572 sheet: -0.11 (0.29), residues: 296 loop : -1.05 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 355 HIS 0.005 0.001 HIS B 100 PHE 0.011 0.001 PHE C 265 TYR 0.017 0.002 TYR A 239 ARG 0.008 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 140 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4491 (mmp) cc_final: 0.2907 (mtm) REVERT: A 46 MET cc_start: 0.2174 (OUTLIER) cc_final: 0.1968 (tpt) REVERT: A 49 LYS cc_start: 0.5554 (mtpp) cc_final: 0.5184 (ptmt) REVERT: A 147 THR cc_start: 0.8229 (p) cc_final: 0.7974 (m) REVERT: A 183 ASP cc_start: 0.7098 (m-30) cc_final: 0.6803 (m-30) REVERT: A 190 LYS cc_start: 0.7267 (ttmt) cc_final: 0.6340 (mttt) REVERT: A 240 GLU cc_start: 0.6313 (mt-10) cc_final: 0.5882 (tt0) REVERT: A 271 CYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7117 (p) REVERT: A 275 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6526 (mm-30) REVERT: A 287 ASP cc_start: 0.7241 (t70) cc_final: 0.6846 (t70) REVERT: A 312 MET cc_start: 0.8307 (tpp) cc_final: 0.8041 (tpt) REVERT: A 313 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: A 327 LYS cc_start: 0.6667 (mttp) cc_final: 0.6367 (mptp) REVERT: B 46 MET cc_start: 0.2982 (mmm) cc_final: 0.2360 (tmm) REVERT: B 49 LYS cc_start: 0.7397 (mtpp) cc_final: 0.6448 (mppt) REVERT: B 67 LYS cc_start: 0.7542 (mttm) cc_final: 0.6931 (mtmm) REVERT: B 81 MET cc_start: 0.7139 (tpt) cc_final: 0.6872 (tpp) REVERT: B 90 TYR cc_start: 0.7838 (m-80) cc_final: 0.7343 (m-80) REVERT: B 94 ARG cc_start: 0.7386 (mtt180) cc_final: 0.6495 (mtm110) REVERT: B 116 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6209 (mt-10) REVERT: B 124 GLU cc_start: 0.5954 (mt-10) cc_final: 0.5341 (pt0) REVERT: B 182 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6617 (ttm170) REVERT: B 271 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7519 (p) REVERT: B 327 LYS cc_start: 0.7514 (mttp) cc_final: 0.7157 (mttt) REVERT: C 46 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.4646 (tpp) REVERT: C 49 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7568 (mttm) REVERT: C 94 ARG cc_start: 0.7454 (mmm160) cc_final: 0.7018 (mtm110) REVERT: C 275 GLU cc_start: 0.7116 (tp30) cc_final: 0.6667 (tt0) REVERT: C 313 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7382 (tp40) REVERT: C 323 THR cc_start: 0.7074 (OUTLIER) cc_final: 0.6719 (p) REVERT: C 327 LYS cc_start: 0.7176 (mttp) cc_final: 0.6791 (mtmp) REVERT: C 362 ASP cc_start: 0.6894 (t0) cc_final: 0.5811 (m-30) REVERT: D 49 LYS cc_start: 0.6889 (mtpp) cc_final: 0.6363 (mmtm) REVERT: D 50 ASP cc_start: 0.6870 (m-30) cc_final: 0.6531 (p0) REVERT: D 82 GLU cc_start: 0.6707 (pp20) cc_final: 0.6313 (pp20) REVERT: D 98 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: D 124 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6060 (pt0) REVERT: D 152 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7515 (tpt) REVERT: D 271 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7481 (p) REVERT: D 315 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6013 (mt-10) REVERT: D 352 GLN cc_start: 0.7412 (mm110) cc_final: 0.7077 (mm-40) REVERT: D 362 ASP cc_start: 0.6277 (t0) cc_final: 0.5541 (p0) outliers start: 53 outliers final: 32 residues processed: 175 average time/residue: 1.2433 time to fit residues: 235.3691 Evaluate side-chains 182 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 139 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 347 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 120 GLN D 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12052 Z= 0.154 Angle : 0.538 9.004 16352 Z= 0.258 Chirality : 0.043 0.133 1812 Planarity : 0.004 0.064 2096 Dihedral : 10.592 158.132 1684 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.72 % Allowed : 22.86 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1476 helix: 0.44 (0.23), residues: 552 sheet: 0.06 (0.30), residues: 296 loop : -0.72 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 355 HIS 0.003 0.001 HIS B 100 PHE 0.007 0.001 PHE D 30 TYR 0.013 0.001 TYR A 239 ARG 0.006 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4499 (mmp) cc_final: 0.2836 (mtm) REVERT: A 49 LYS cc_start: 0.5434 (mtpp) cc_final: 0.5026 (ptmt) REVERT: A 65 THR cc_start: 0.7048 (OUTLIER) cc_final: 0.6754 (p) REVERT: A 147 THR cc_start: 0.8139 (p) cc_final: 0.7911 (m) REVERT: A 183 ASP cc_start: 0.7172 (m-30) cc_final: 0.6882 (m-30) REVERT: A 190 LYS cc_start: 0.7208 (ttmt) cc_final: 0.6299 (mttt) REVERT: A 240 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5814 (tt0) REVERT: A 271 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7125 (p) REVERT: A 275 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6515 (mm-30) REVERT: A 287 ASP cc_start: 0.7217 (t70) cc_final: 0.6820 (t70) REVERT: A 312 MET cc_start: 0.8234 (tpp) cc_final: 0.7973 (tpt) REVERT: A 313 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: A 327 LYS cc_start: 0.6636 (mttp) cc_final: 0.6336 (mptp) REVERT: B 15 MET cc_start: 0.7920 (mmm) cc_final: 0.7571 (mtt) REVERT: B 46 MET cc_start: 0.3057 (mmm) cc_final: 0.2382 (tmm) REVERT: B 49 LYS cc_start: 0.7413 (mtpp) cc_final: 0.6471 (mppt) REVERT: B 67 LYS cc_start: 0.7572 (mttm) cc_final: 0.6957 (mtmm) REVERT: B 81 MET cc_start: 0.7006 (tpt) cc_final: 0.6789 (tpp) REVERT: B 90 TYR cc_start: 0.7747 (m-80) cc_final: 0.7227 (m-80) REVERT: B 94 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6483 (mtm110) REVERT: B 116 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6019 (mt-10) REVERT: B 124 GLU cc_start: 0.6078 (mt-10) cc_final: 0.5469 (pt0) REVERT: B 147 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8246 (t) REVERT: B 182 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6610 (ttm170) REVERT: B 249 ILE cc_start: 0.7877 (mt) cc_final: 0.7491 (tt) REVERT: B 271 CYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7550 (p) REVERT: B 327 LYS cc_start: 0.7494 (mttp) cc_final: 0.7081 (mttt) REVERT: B 357 SER cc_start: 0.7921 (m) cc_final: 0.7585 (t) REVERT: C 46 MET cc_start: 0.5077 (OUTLIER) cc_final: 0.4606 (tpp) REVERT: C 49 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7549 (mttm) REVERT: C 94 ARG cc_start: 0.7429 (mmm160) cc_final: 0.6981 (mtm110) REVERT: C 271 CYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7585 (p) REVERT: C 275 GLU cc_start: 0.7090 (tp30) cc_final: 0.6734 (tt0) REVERT: C 313 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7176 (tp40) REVERT: C 323 THR cc_start: 0.7089 (m) cc_final: 0.6718 (p) REVERT: C 327 LYS cc_start: 0.7152 (mttp) cc_final: 0.6769 (mtmp) REVERT: C 362 ASP cc_start: 0.6888 (t0) cc_final: 0.5795 (m-30) REVERT: D 49 LYS cc_start: 0.6882 (mtpp) cc_final: 0.6348 (mmtm) REVERT: D 50 ASP cc_start: 0.6853 (m-30) cc_final: 0.6529 (p0) REVERT: D 82 GLU cc_start: 0.6804 (pp20) cc_final: 0.6487 (pt0) REVERT: D 98 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6205 (mp0) REVERT: D 124 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6078 (pt0) REVERT: D 152 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7495 (tpt) REVERT: D 200 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8404 (m) REVERT: D 271 CYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7431 (p) REVERT: D 315 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6075 (mm-30) REVERT: D 325 LYS cc_start: 0.6720 (mttt) cc_final: 0.6252 (mppt) REVERT: D 352 GLN cc_start: 0.7406 (mm110) cc_final: 0.7077 (mm-40) REVERT: D 362 ASP cc_start: 0.6161 (t0) cc_final: 0.5364 (m-30) outliers start: 47 outliers final: 24 residues processed: 174 average time/residue: 1.2667 time to fit residues: 238.0975 Evaluate side-chains 177 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 347 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN D 11 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12052 Z= 0.169 Angle : 0.546 9.103 16352 Z= 0.261 Chirality : 0.043 0.137 1812 Planarity : 0.004 0.065 2096 Dihedral : 10.373 163.486 1684 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.40 % Allowed : 23.73 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1476 helix: 0.40 (0.23), residues: 560 sheet: 0.21 (0.30), residues: 292 loop : -0.64 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 355 HIS 0.002 0.001 HIS A 160 PHE 0.007 0.001 PHE B 222 TYR 0.014 0.001 TYR A 239 ARG 0.007 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4656 (mmp) cc_final: 0.3013 (mtm) REVERT: A 49 LYS cc_start: 0.5427 (mtpp) cc_final: 0.5035 (ptmt) REVERT: A 65 THR cc_start: 0.7030 (OUTLIER) cc_final: 0.6731 (p) REVERT: A 147 THR cc_start: 0.8139 (p) cc_final: 0.7928 (m) REVERT: A 183 ASP cc_start: 0.7180 (m-30) cc_final: 0.6890 (m-30) REVERT: A 190 LYS cc_start: 0.7215 (ttmt) cc_final: 0.6306 (mttt) REVERT: A 240 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5819 (tt0) REVERT: A 271 CYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7141 (p) REVERT: A 275 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6463 (mm-30) REVERT: A 287 ASP cc_start: 0.7214 (t70) cc_final: 0.6817 (t70) REVERT: A 312 MET cc_start: 0.8243 (tpp) cc_final: 0.7983 (tpt) REVERT: A 313 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: B 46 MET cc_start: 0.3059 (mmm) cc_final: 0.2507 (tmm) REVERT: B 49 LYS cc_start: 0.7402 (mtpp) cc_final: 0.6458 (mppt) REVERT: B 67 LYS cc_start: 0.7562 (mttm) cc_final: 0.6957 (mtmm) REVERT: B 81 MET cc_start: 0.7003 (tpt) cc_final: 0.6793 (tpp) REVERT: B 90 TYR cc_start: 0.7760 (m-80) cc_final: 0.7314 (m-80) REVERT: B 94 ARG cc_start: 0.7340 (mtt180) cc_final: 0.6494 (mtm110) REVERT: B 116 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6014 (mt-10) REVERT: B 124 GLU cc_start: 0.6123 (mt-10) cc_final: 0.5488 (pt0) REVERT: B 147 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8278 (t) REVERT: B 249 ILE cc_start: 0.7899 (mt) cc_final: 0.7510 (tt) REVERT: B 271 CYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7591 (p) REVERT: B 327 LYS cc_start: 0.7492 (mttp) cc_final: 0.7081 (mttt) REVERT: B 357 SER cc_start: 0.7901 (m) cc_final: 0.7572 (t) REVERT: C 46 MET cc_start: 0.5111 (OUTLIER) cc_final: 0.4653 (tpp) REVERT: C 49 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7520 (mttm) REVERT: C 94 ARG cc_start: 0.7418 (mmm160) cc_final: 0.6985 (mtm110) REVERT: C 271 CYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7602 (p) REVERT: C 275 GLU cc_start: 0.7090 (tp30) cc_final: 0.6731 (tt0) REVERT: C 327 LYS cc_start: 0.7130 (mttp) cc_final: 0.6756 (mtmp) REVERT: C 362 ASP cc_start: 0.6896 (t0) cc_final: 0.5806 (m-30) REVERT: D 49 LYS cc_start: 0.6771 (mtpp) cc_final: 0.6232 (mmtm) REVERT: D 50 ASP cc_start: 0.6861 (m-30) cc_final: 0.6541 (p0) REVERT: D 82 GLU cc_start: 0.6739 (pp20) cc_final: 0.6396 (pt0) REVERT: D 98 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6214 (mp0) REVERT: D 124 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6128 (pt0) REVERT: D 152 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7499 (tpt) REVERT: D 200 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8426 (m) REVERT: D 315 GLU cc_start: 0.6527 (mm-30) cc_final: 0.5886 (mt-10) REVERT: D 325 LYS cc_start: 0.6747 (mttt) cc_final: 0.6254 (mppt) REVERT: D 352 GLN cc_start: 0.7425 (mm110) cc_final: 0.7102 (mm-40) REVERT: D 362 ASP cc_start: 0.6169 (t0) cc_final: 0.5475 (m-30) outliers start: 43 outliers final: 25 residues processed: 165 average time/residue: 1.2925 time to fit residues: 233.8755 Evaluate side-chains 174 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain D residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 135 optimal weight: 0.0270 chunk 117 optimal weight: 0.0270 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12052 Z= 0.151 Angle : 0.531 9.510 16352 Z= 0.251 Chirality : 0.042 0.138 1812 Planarity : 0.004 0.066 2096 Dihedral : 10.079 173.479 1684 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.93 % Allowed : 24.29 % Favored : 72.78 % 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: -0.04 (0.22), residues: 1476 helix: 0.48 (0.23), residues: 560 sheet: 0.28 (0.30), residues: 292 loop : -0.52 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 355 HIS 0.002 0.001 HIS A 160 PHE 0.011 0.001 PHE A 278 TYR 0.013 0.001 TYR A 239 ARG 0.007 0.000 ARG D 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.4538 (mmp) cc_final: 0.2887 (mtm) REVERT: A 49 LYS cc_start: 0.5440 (mtpp) cc_final: 0.5102 (ptmt) REVERT: A 65 THR cc_start: 0.6970 (OUTLIER) cc_final: 0.6686 (p) REVERT: A 183 ASP cc_start: 0.7174 (m-30) cc_final: 0.6884 (m-30) REVERT: A 190 LYS cc_start: 0.7218 (ttmt) cc_final: 0.6281 (mttt) REVERT: A 240 GLU cc_start: 0.6137 (mt-10) cc_final: 0.5785 (tt0) REVERT: A 271 CYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7166 (p) REVERT: A 275 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6446 (mm-30) REVERT: A 287 ASP cc_start: 0.7176 (t70) cc_final: 0.6773 (t70) REVERT: A 312 MET cc_start: 0.8233 (tpp) cc_final: 0.7978 (tpt) REVERT: A 351 PHE cc_start: 0.8125 (t80) cc_final: 0.7887 (t80) REVERT: B 15 MET cc_start: 0.7911 (mmm) cc_final: 0.7556 (mtt) REVERT: B 46 MET cc_start: 0.2974 (mmm) cc_final: 0.2511 (tmm) REVERT: B 49 LYS cc_start: 0.7406 (mtpp) cc_final: 0.6451 (mppt) REVERT: B 67 LYS cc_start: 0.7577 (mttm) cc_final: 0.6967 (mtmm) REVERT: B 81 MET cc_start: 0.6939 (tpt) cc_final: 0.6738 (tpp) REVERT: B 90 TYR cc_start: 0.7742 (m-80) cc_final: 0.7226 (m-80) REVERT: B 94 ARG cc_start: 0.7364 (mtt180) cc_final: 0.6505 (mtm110) REVERT: B 116 GLU cc_start: 0.6370 (mt-10) cc_final: 0.5992 (mt-10) REVERT: B 147 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8337 (t) REVERT: B 271 CYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7620 (p) REVERT: B 327 LYS cc_start: 0.7497 (mttp) cc_final: 0.7089 (mttt) REVERT: B 357 SER cc_start: 0.7834 (m) cc_final: 0.7562 (t) REVERT: C 46 MET cc_start: 0.5018 (OUTLIER) cc_final: 0.4569 (tpp) REVERT: C 49 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7553 (mttm) REVERT: C 94 ARG cc_start: 0.7406 (mmm160) cc_final: 0.6970 (mtm110) REVERT: C 275 GLU cc_start: 0.7068 (tp30) cc_final: 0.6698 (tt0) REVERT: C 327 LYS cc_start: 0.7098 (mttp) cc_final: 0.6727 (mtmp) REVERT: C 362 ASP cc_start: 0.6896 (t0) cc_final: 0.5804 (m-30) REVERT: D 49 LYS cc_start: 0.6746 (mtpp) cc_final: 0.6224 (mmtm) REVERT: D 50 ASP cc_start: 0.6868 (m-30) cc_final: 0.6544 (p0) REVERT: D 82 GLU cc_start: 0.6733 (pp20) cc_final: 0.6410 (pt0) REVERT: D 124 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6139 (pt0) REVERT: D 315 GLU cc_start: 0.6469 (mm-30) cc_final: 0.5833 (mt-10) REVERT: D 325 LYS cc_start: 0.6672 (mttt) cc_final: 0.6235 (mppt) REVERT: D 352 GLN cc_start: 0.7473 (mm110) cc_final: 0.7151 (mm-40) REVERT: D 362 ASP cc_start: 0.6153 (t0) cc_final: 0.5481 (m-30) outliers start: 37 outliers final: 22 residues processed: 165 average time/residue: 1.3093 time to fit residues: 234.3050 Evaluate side-chains 161 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 0.0010 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127782 restraints weight = 15875.241| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.76 r_work: 0.3578 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12052 Z= 0.173 Angle : 0.539 9.864 16352 Z= 0.257 Chirality : 0.043 0.146 1812 Planarity : 0.004 0.065 2096 Dihedral : 9.841 170.327 1684 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.37 % Allowed : 25.16 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1476 helix: 0.50 (0.23), residues: 560 sheet: 0.30 (0.30), residues: 292 loop : -0.53 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 355 HIS 0.002 0.001 HIS A 160 PHE 0.008 0.001 PHE A 278 TYR 0.014 0.001 TYR A 239 ARG 0.007 0.000 ARG D 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4401.31 seconds wall clock time: 78 minutes 58.91 seconds (4738.91 seconds total)