Starting phenix.real_space_refine on Fri Feb 16 21:17:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sni_25227/02_2024/7sni_25227_updated.pdb" } resolution = 2.5 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= 0.010 sd= 0.218 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: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 80 5.16 5 C 10312 2.51 5 N 2816 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 473": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 473": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16533 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3963 Classifications: {'peptide': 488} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 463} Chain: "B" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3963 Classifications: {'peptide': 488} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 463} Chain: "C" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3963 Classifications: {'peptide': 488} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 463} Chain: "D" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3963 Classifications: {'peptide': 488} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 463} Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'BG6': 1, 'NAP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Time building chain proxies: 9.23, per 1000 atoms: 0.56 Number of scatterers: 16533 At special positions: 0 Unit cell: (131.97, 102.09, 115.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 28 15.00 O 3297 8.00 N 2816 7.00 C 10312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.37 Conformation dependent library (CDL) restraints added in 3.0 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 8 sheets defined 37.2% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 42 through 57 removed outlier: 5.474A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 77 through 88 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 92 through 104 removed outlier: 3.537A pdb=" N LYS A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 144 through 157 removed outlier: 5.188A pdb=" N GLU A 148 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 157 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.580A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 206 through 216 removed outlier: 4.401A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.803A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.675A pdb=" N CYS A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 455 through 475 removed outlier: 3.622A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'B' and resid 42 through 57 removed outlier: 5.469A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 77 through 88 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 92 through 104 removed outlier: 5.225A pdb=" N LEU B 96 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'B' and resid 144 through 157 removed outlier: 5.104A pdb=" N GLU B 148 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 157 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.617A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 206 through 216 removed outlier: 4.406A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 259 removed outlier: 3.807A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N ILE B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.656A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 455 through 475 removed outlier: 3.616A pdb=" N PHE B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'C' and resid 42 through 57 removed outlier: 5.468A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 77 through 88 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 92 through 104 removed outlier: 3.540A pdb=" N LYS C 95 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 144 through 157 removed outlier: 5.101A pdb=" N GLU C 148 " --> pdb=" O THR C 145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 157 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.625A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'C' and resid 206 through 216 removed outlier: 4.405A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.659A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 436 through 446 Processing helix chain 'C' and resid 455 through 475 removed outlier: 3.614A pdb=" N PHE C 465 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'D' and resid 42 through 57 removed outlier: 5.468A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 77 through 88 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 92 through 103 removed outlier: 3.521A pdb=" N LYS D 95 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU D 96 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 144 through 157 removed outlier: 5.107A pdb=" N GLU D 148 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 157 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.623A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 190 " --> pdb=" O HIS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.409A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 263 through 272 Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.637A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 436 through 446 Processing helix chain 'D' and resid 455 through 475 removed outlier: 3.621A pdb=" N PHE D 465 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 490 through 499 Processing sheet with id= A, first strand: chain 'A' and resid 196 through 198 removed outlier: 8.155A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG A 136 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ILE A 168 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 138 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 71 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 480 through 483 removed outlier: 3.569A pdb=" N GLN A 307 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 482 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLN A 372 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 233 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG A 370 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 235 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 368 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE A 237 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS A 366 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 369 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG A 393 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 371 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL A 391 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 373 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 389 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 196 through 198 removed outlier: 8.131A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 71 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 480 through 483 removed outlier: 3.566A pdb=" N GLN B 307 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 482 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN B 372 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL B 233 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG B 370 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 235 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B 368 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 237 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS B 366 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 369 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG B 393 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 371 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL B 391 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE B 373 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 389 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 196 through 198 removed outlier: 8.115A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 71 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 480 through 483 removed outlier: 3.563A pdb=" N GLN C 307 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 482 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN C 372 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 233 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG C 370 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 235 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU C 368 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 237 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS C 366 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 369 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG C 393 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 371 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL C 391 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE C 373 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU C 389 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 196 through 198 removed outlier: 8.129A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 71 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 480 through 483 removed outlier: 3.565A pdb=" N GLN D 307 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 482 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN D 372 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL D 233 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG D 370 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU D 235 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU D 368 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE D 237 " --> pdb=" O LYS D 366 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS D 366 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL D 369 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG D 393 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU D 371 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL D 391 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE D 373 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU D 389 " --> pdb=" O PHE D 373 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3372 1.33 - 1.45: 3988 1.45 - 1.57: 9180 1.57 - 1.69: 44 1.69 - 1.81: 132 Bond restraints: 16716 Sorted by residual: bond pdb=" O2B NAP B 602 " pdb=" P2B NAP B 602 " ideal model delta sigma weight residual 1.736 1.588 0.148 2.00e-02 2.50e+03 5.44e+01 bond pdb=" O2B NAP C 602 " pdb=" P2B NAP C 602 " ideal model delta sigma weight residual 1.736 1.589 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" O2B NAP D 602 " pdb=" P2B NAP D 602 " ideal model delta sigma weight residual 1.736 1.589 0.147 2.00e-02 2.50e+03 5.40e+01 bond pdb=" O2B NAP A 602 " pdb=" P2B NAP A 602 " ideal model delta sigma weight residual 1.736 1.589 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O2B NAP B 601 " pdb=" P2B NAP B 601 " ideal model delta sigma weight residual 1.736 1.602 0.134 2.00e-02 2.50e+03 4.46e+01 ... (remaining 16711 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.78: 616 106.78 - 114.22: 9462 114.22 - 121.65: 8878 121.65 - 129.09: 3608 129.09 - 136.53: 132 Bond angle restraints: 22696 Sorted by residual: angle pdb=" N ASP D 313 " pdb=" CA ASP D 313 " pdb=" C ASP D 313 " ideal model delta sigma weight residual 113.21 105.47 7.74 1.15e+00 7.56e-01 4.53e+01 angle pdb=" N GLY D 314 " pdb=" CA GLY D 314 " pdb=" C GLY D 314 " ideal model delta sigma weight residual 112.54 120.06 -7.52 1.28e+00 6.10e-01 3.45e+01 angle pdb=" N ASP B 313 " pdb=" CA ASP B 313 " pdb=" C ASP B 313 " ideal model delta sigma weight residual 112.92 106.49 6.43 1.23e+00 6.61e-01 2.73e+01 angle pdb=" N ASP A 313 " pdb=" CA ASP A 313 " pdb=" C ASP A 313 " ideal model delta sigma weight residual 112.92 106.63 6.29 1.23e+00 6.61e-01 2.62e+01 angle pdb=" N ASP C 313 " pdb=" CA ASP C 313 " pdb=" C ASP C 313 " ideal model delta sigma weight residual 112.92 106.67 6.25 1.23e+00 6.61e-01 2.58e+01 ... (remaining 22691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.59: 9349 23.59 - 47.18: 779 47.18 - 70.78: 134 70.78 - 94.37: 42 94.37 - 117.96: 20 Dihedral angle restraints: 10324 sinusoidal: 4636 harmonic: 5688 Sorted by residual: dihedral pdb=" CA ILE A 199 " pdb=" C ILE A 199 " pdb=" N ASN A 200 " pdb=" CA ASN A 200 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C1 BG6 A 603 " pdb=" C5 BG6 A 603 " pdb=" O5 BG6 A 603 " pdb=" C4 BG6 A 603 " ideal model delta sinusoidal sigma weight residual 53.02 -64.94 117.96 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C3 BG6 A 603 " pdb=" C1 BG6 A 603 " pdb=" C2 BG6 A 603 " pdb=" O5 BG6 A 603 " ideal model delta sinusoidal sigma weight residual 52.85 -61.57 114.42 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 10321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1758 0.044 - 0.089: 465 0.089 - 0.133: 164 0.133 - 0.178: 13 0.178 - 0.222: 16 Chirality restraints: 2416 Sorted by residual: chirality pdb=" C1B NAP C 602 " pdb=" C2B NAP C 602 " pdb=" N9A NAP C 602 " pdb=" O4B NAP C 602 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1B NAP B 602 " pdb=" C2B NAP B 602 " pdb=" N9A NAP B 602 " pdb=" O4B NAP B 602 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C1B NAP A 602 " pdb=" C2B NAP A 602 " pdb=" N9A NAP A 602 " pdb=" O4B NAP A 602 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2413 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 95 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C LYS D 95 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS D 95 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU D 96 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 222 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 223 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 222 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO D 223 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.022 5.00e-02 4.00e+02 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3124 2.77 - 3.30: 16146 3.30 - 3.84: 30820 3.84 - 4.37: 37857 4.37 - 4.90: 61224 Nonbonded interactions: 149171 Sorted by model distance: nonbonded pdb=" O TRP D 462 " pdb=" OG1 THR D 466 " model vdw 2.239 2.440 nonbonded pdb=" O TRP C 462 " pdb=" OG1 THR C 466 " model vdw 2.239 2.440 nonbonded pdb=" O TRP B 462 " pdb=" OG1 THR B 466 " model vdw 2.241 2.440 nonbonded pdb=" O TRP A 462 " pdb=" OG1 THR A 466 " model vdw 2.243 2.440 nonbonded pdb=" O GLY C 316 " pdb=" OG1 THR C 319 " model vdw 2.243 2.440 ... (remaining 149166 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.320 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 47.420 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 0.148 16716 Z= 0.407 Angle : 0.743 8.995 22696 Z= 0.348 Chirality : 0.047 0.222 2416 Planarity : 0.004 0.039 2892 Dihedral : 17.947 117.960 6668 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.06 % Allowed : 0.53 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1944 helix: 0.55 (0.20), residues: 704 sheet: -0.81 (0.25), residues: 428 loop : 0.17 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 225 HIS 0.007 0.001 HIS A 186 PHE 0.011 0.001 PHE C 452 TYR 0.013 0.001 TYR D 202 ARG 0.005 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 1.885 Fit side-chains REVERT: A 443 ASP cc_start: 0.7456 (m-30) cc_final: 0.7225 (m-30) REVERT: B 443 ASP cc_start: 0.7450 (m-30) cc_final: 0.7230 (m-30) REVERT: C 443 ASP cc_start: 0.7456 (m-30) cc_final: 0.7231 (m-30) REVERT: D 443 ASP cc_start: 0.7438 (m-30) cc_final: 0.7228 (m-30) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 1.4370 time to fit residues: 420.7429 Evaluate side-chains 202 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 0.0030 chunk 150 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 105 ASN B 186 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 186 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 186 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16716 Z= 0.312 Angle : 0.619 5.891 22696 Z= 0.326 Chirality : 0.047 0.144 2416 Planarity : 0.006 0.047 2892 Dihedral : 16.558 104.403 2724 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.16 % Allowed : 8.06 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.35 (0.19), residues: 1944 helix: 0.14 (0.20), residues: 712 sheet: -0.97 (0.25), residues: 376 loop : 0.01 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 225 HIS 0.003 0.001 HIS A 186 PHE 0.016 0.002 PHE D 452 TYR 0.021 0.002 TYR C 484 ARG 0.006 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 1.937 Fit side-chains REVERT: A 152 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7716 (ptmt) REVERT: A 212 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7644 (tpp) REVERT: A 443 ASP cc_start: 0.7579 (m-30) cc_final: 0.7328 (m-30) REVERT: B 152 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7717 (ptmt) REVERT: B 212 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7484 (ttm) REVERT: B 443 ASP cc_start: 0.7569 (m-30) cc_final: 0.7303 (m-30) REVERT: C 152 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7739 (ptmt) REVERT: C 212 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7486 (ttm) REVERT: C 443 ASP cc_start: 0.7577 (m-30) cc_final: 0.7298 (m-30) REVERT: D 104 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7148 (ptm160) REVERT: D 152 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7773 (ptmt) REVERT: D 212 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7476 (ttm) REVERT: D 443 ASP cc_start: 0.7569 (m-30) cc_final: 0.7310 (m-30) outliers start: 37 outliers final: 12 residues processed: 237 average time/residue: 1.4431 time to fit residues: 377.4828 Evaluate side-chains 229 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 105 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 105 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 186 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16716 Z= 0.409 Angle : 0.664 6.791 22696 Z= 0.351 Chirality : 0.049 0.149 2416 Planarity : 0.006 0.051 2892 Dihedral : 16.544 106.236 2724 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.57 % Allowed : 10.86 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.61 (0.19), residues: 1944 helix: -0.12 (0.20), residues: 712 sheet: -1.05 (0.25), residues: 376 loop : -0.11 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 164 HIS 0.005 0.001 HIS D 374 PHE 0.017 0.002 PHE D 452 TYR 0.023 0.003 TYR C 484 ARG 0.005 0.001 ARG C 463 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 1.893 Fit side-chains REVERT: A 152 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7721 (ptmt) REVERT: A 212 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7517 (ttm) REVERT: A 443 ASP cc_start: 0.7678 (m-30) cc_final: 0.7444 (m-30) REVERT: B 152 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7745 (ptmt) REVERT: B 212 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7522 (ttm) REVERT: B 443 ASP cc_start: 0.7647 (m-30) cc_final: 0.7413 (m-30) REVERT: C 152 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7731 (ptmt) REVERT: C 212 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7523 (ttm) REVERT: C 443 ASP cc_start: 0.7654 (m-30) cc_final: 0.7414 (m-30) REVERT: D 104 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7240 (ptm160) REVERT: D 152 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7773 (ptmt) REVERT: D 212 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7552 (ttm) REVERT: D 443 ASP cc_start: 0.7677 (m-30) cc_final: 0.7437 (m-30) outliers start: 44 outliers final: 17 residues processed: 232 average time/residue: 1.3720 time to fit residues: 351.7616 Evaluate side-chains 227 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 307 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 186 HIS B 307 GLN ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 105 ASN C 186 HIS C 307 GLN ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 105 ASN D 186 HIS D 307 GLN D 426 ASN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16716 Z= 0.193 Angle : 0.541 5.256 22696 Z= 0.285 Chirality : 0.044 0.138 2416 Planarity : 0.005 0.048 2892 Dihedral : 15.645 103.669 2724 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.10 % Allowed : 11.97 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.30 (0.19), residues: 1944 helix: 0.21 (0.20), residues: 704 sheet: -0.90 (0.26), residues: 372 loop : -0.00 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 164 HIS 0.003 0.001 HIS C 451 PHE 0.013 0.001 PHE C 452 TYR 0.016 0.001 TYR C 308 ARG 0.004 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 1.890 Fit side-chains REVERT: A 152 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7681 (ptmt) REVERT: A 404 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7294 (ppp) REVERT: A 443 ASP cc_start: 0.7629 (m-30) cc_final: 0.7343 (m-30) REVERT: B 152 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7693 (ptmt) REVERT: B 443 ASP cc_start: 0.7647 (m-30) cc_final: 0.7376 (m-30) REVERT: C 64 ASN cc_start: 0.7414 (m110) cc_final: 0.7185 (m110) REVERT: C 152 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7701 (ptmt) REVERT: C 443 ASP cc_start: 0.7657 (m-30) cc_final: 0.7376 (m-30) REVERT: D 104 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7155 (ptm160) REVERT: D 152 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7714 (ptmt) REVERT: D 443 ASP cc_start: 0.7660 (m-30) cc_final: 0.7391 (m-30) outliers start: 36 outliers final: 17 residues processed: 239 average time/residue: 1.4281 time to fit residues: 376.6223 Evaluate side-chains 231 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 40.0000 chunk 105 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 384 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN A 471 GLN B 105 ASN B 126 ASN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN C 471 GLN D 105 ASN ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 426 ASN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 16716 Z= 0.510 Angle : 0.735 7.251 22696 Z= 0.386 Chirality : 0.051 0.175 2416 Planarity : 0.006 0.053 2892 Dihedral : 16.262 107.312 2724 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.86 % Allowed : 12.73 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.83 (0.19), residues: 1944 helix: -0.33 (0.19), residues: 712 sheet: -1.12 (0.25), residues: 384 loop : -0.23 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 164 HIS 0.004 0.001 HIS A 186 PHE 0.020 0.003 PHE A 452 TYR 0.024 0.003 TYR A 484 ARG 0.006 0.001 ARG C 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 2.242 Fit side-chains REVERT: A 152 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7728 (ptmt) REVERT: A 212 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7491 (ttm) REVERT: A 443 ASP cc_start: 0.7714 (m-30) cc_final: 0.7497 (m-30) REVERT: B 152 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7713 (ptmt) REVERT: B 212 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7491 (ttm) REVERT: B 443 ASP cc_start: 0.7706 (m-30) cc_final: 0.7495 (m-30) REVERT: C 152 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7709 (ptmt) REVERT: C 212 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7492 (ttm) REVERT: C 443 ASP cc_start: 0.7713 (m-30) cc_final: 0.7495 (m-30) REVERT: D 104 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7211 (ptm160) REVERT: D 152 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7738 (ptmt) REVERT: D 212 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7492 (ttm) REVERT: D 443 ASP cc_start: 0.7708 (m-30) cc_final: 0.7494 (m-30) outliers start: 49 outliers final: 24 residues processed: 243 average time/residue: 1.4296 time to fit residues: 382.8974 Evaluate side-chains 237 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 424 TYR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 471 GLN Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 186 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 105 ASN B 186 HIS ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 105 ASN C 186 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 126 ASN D 186 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16716 Z= 0.225 Angle : 0.569 5.529 22696 Z= 0.300 Chirality : 0.044 0.139 2416 Planarity : 0.005 0.050 2892 Dihedral : 15.459 103.413 2724 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.28 % Allowed : 14.66 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.47 (0.19), residues: 1944 helix: 0.06 (0.20), residues: 712 sheet: -0.96 (0.25), residues: 376 loop : -0.10 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 164 HIS 0.003 0.001 HIS A 451 PHE 0.015 0.001 PHE A 452 TYR 0.018 0.002 TYR C 308 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 1.902 Fit side-chains REVERT: A 152 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7673 (ptmt) REVERT: A 443 ASP cc_start: 0.7633 (m-30) cc_final: 0.7355 (m-30) REVERT: B 152 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7689 (ptmt) REVERT: B 443 ASP cc_start: 0.7628 (m-30) cc_final: 0.7370 (m-30) REVERT: C 152 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7681 (ptmt) REVERT: C 443 ASP cc_start: 0.7639 (m-30) cc_final: 0.7367 (m-30) REVERT: D 104 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7136 (ptm160) REVERT: D 152 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7698 (ptmt) REVERT: D 443 ASP cc_start: 0.7641 (m-30) cc_final: 0.7373 (m-30) outliers start: 39 outliers final: 15 residues processed: 236 average time/residue: 1.4735 time to fit residues: 382.5400 Evaluate side-chains 226 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 186 HIS B 426 ASN ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 105 ASN C 126 ASN C 186 HIS C 426 ASN ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 186 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16716 Z= 0.223 Angle : 0.560 5.338 22696 Z= 0.295 Chirality : 0.044 0.138 2416 Planarity : 0.005 0.050 2892 Dihedral : 15.257 104.277 2724 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.51 % Allowed : 15.19 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.34 (0.19), residues: 1944 helix: 0.17 (0.20), residues: 712 sheet: -0.91 (0.26), residues: 376 loop : -0.02 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 164 HIS 0.003 0.001 HIS A 186 PHE 0.013 0.001 PHE A 452 TYR 0.018 0.002 TYR C 308 ARG 0.003 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 1.745 Fit side-chains REVERT: A 152 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7695 (ptmt) REVERT: A 443 ASP cc_start: 0.7598 (m-30) cc_final: 0.7315 (m-30) REVERT: B 152 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7703 (ptmt) REVERT: B 443 ASP cc_start: 0.7606 (m-30) cc_final: 0.7339 (m-30) REVERT: C 64 ASN cc_start: 0.7465 (m110) cc_final: 0.7219 (m110) REVERT: C 152 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7702 (ptmt) REVERT: C 443 ASP cc_start: 0.7619 (m-30) cc_final: 0.7322 (m-30) REVERT: D 104 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7212 (ptm160) REVERT: D 152 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7724 (ptmt) REVERT: D 443 ASP cc_start: 0.7602 (m-30) cc_final: 0.7334 (m-30) outliers start: 43 outliers final: 18 residues processed: 241 average time/residue: 1.3572 time to fit residues: 362.0535 Evaluate side-chains 234 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 117 optimal weight: 0.3980 chunk 126 optimal weight: 0.0670 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 186 HIS ** B 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 186 HIS ** C 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 186 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16716 Z= 0.187 Angle : 0.542 5.209 22696 Z= 0.285 Chirality : 0.043 0.136 2416 Planarity : 0.005 0.047 2892 Dihedral : 14.737 103.788 2724 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.10 % Allowed : 16.36 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.24 (0.19), residues: 1944 helix: 0.24 (0.21), residues: 712 sheet: -0.86 (0.26), residues: 376 loop : 0.06 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 164 HIS 0.003 0.001 HIS C 451 PHE 0.014 0.001 PHE B 66 TYR 0.017 0.001 TYR C 308 ARG 0.002 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.967 Fit side-chains REVERT: A 152 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7691 (ptmt) REVERT: A 443 ASP cc_start: 0.7596 (m-30) cc_final: 0.7314 (m-30) REVERT: B 152 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7705 (ptmt) REVERT: B 443 ASP cc_start: 0.7611 (m-30) cc_final: 0.7353 (m-30) REVERT: C 64 ASN cc_start: 0.7442 (m110) cc_final: 0.7215 (m110) REVERT: C 152 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7694 (ptmt) REVERT: C 443 ASP cc_start: 0.7625 (m-30) cc_final: 0.7351 (m-30) REVERT: D 64 ASN cc_start: 0.7475 (m110) cc_final: 0.7258 (m110) REVERT: D 152 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7703 (ptmt) REVERT: D 443 ASP cc_start: 0.7588 (m-30) cc_final: 0.7326 (m-30) outliers start: 36 outliers final: 16 residues processed: 245 average time/residue: 1.4140 time to fit residues: 382.9969 Evaluate side-chains 234 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 0.0970 chunk 113 optimal weight: 7.9990 overall best weight: 4.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 186 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 105 ASN B 186 HIS ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 186 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 186 HIS ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16716 Z= 0.308 Angle : 0.603 5.828 22696 Z= 0.317 Chirality : 0.046 0.139 2416 Planarity : 0.005 0.050 2892 Dihedral : 15.210 105.408 2724 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.16 % Allowed : 16.36 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.35 (0.19), residues: 1944 helix: 0.07 (0.20), residues: 716 sheet: -0.89 (0.26), residues: 376 loop : 0.05 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 164 HIS 0.003 0.001 HIS A 186 PHE 0.021 0.002 PHE C 56 TYR 0.020 0.002 TYR B 308 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 1.840 Fit side-chains REVERT: A 152 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7691 (ptmt) REVERT: A 443 ASP cc_start: 0.7604 (m-30) cc_final: 0.7340 (m-30) REVERT: B 152 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7673 (ptmt) REVERT: B 443 ASP cc_start: 0.7595 (m-30) cc_final: 0.7348 (m-30) REVERT: C 152 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7671 (ptmt) REVERT: C 443 ASP cc_start: 0.7608 (m-30) cc_final: 0.7350 (m-30) REVERT: D 152 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7701 (ptmt) REVERT: D 443 ASP cc_start: 0.7583 (m-30) cc_final: 0.7327 (m-30) outliers start: 37 outliers final: 17 residues processed: 232 average time/residue: 1.4089 time to fit residues: 360.8285 Evaluate side-chains 221 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 126 optimal weight: 0.0970 chunk 191 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 152 optimal weight: 40.0000 chunk 15 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 93 optimal weight: 0.0030 chunk 120 optimal weight: 3.9990 overall best weight: 0.6250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 186 HIS ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 105 ASN C 186 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 186 HIS ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16716 Z= 0.133 Angle : 0.519 4.982 22696 Z= 0.271 Chirality : 0.042 0.133 2416 Planarity : 0.004 0.044 2892 Dihedral : 14.169 102.327 2724 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.11 % Allowed : 16.88 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.19), residues: 1944 helix: 0.36 (0.21), residues: 712 sheet: -0.72 (0.27), residues: 368 loop : 0.17 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 164 HIS 0.003 0.001 HIS C 451 PHE 0.016 0.001 PHE B 66 TYR 0.018 0.001 TYR C 308 ARG 0.004 0.000 ARG D 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 1.775 Fit side-chains REVERT: A 152 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7688 (ptmt) REVERT: A 212 MET cc_start: 0.7755 (ttp) cc_final: 0.7003 (ttp) REVERT: A 443 ASP cc_start: 0.7600 (m-30) cc_final: 0.7291 (m-30) REVERT: B 37 MET cc_start: 0.7128 (mmm) cc_final: 0.6898 (mpt) REVERT: B 152 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7681 (ptmt) REVERT: B 443 ASP cc_start: 0.7592 (m-30) cc_final: 0.7283 (m-30) REVERT: C 37 MET cc_start: 0.7127 (mmm) cc_final: 0.6903 (mpt) REVERT: C 64 ASN cc_start: 0.7406 (m110) cc_final: 0.7166 (m110) REVERT: C 152 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7668 (ptmt) REVERT: C 212 MET cc_start: 0.7776 (ttp) cc_final: 0.7035 (ttp) REVERT: C 443 ASP cc_start: 0.7605 (m-30) cc_final: 0.7304 (m-30) REVERT: D 37 MET cc_start: 0.7121 (mmm) cc_final: 0.6890 (mpt) REVERT: D 104 ARG cc_start: 0.7378 (ptp-170) cc_final: 0.6893 (ptm160) REVERT: D 152 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7699 (ptmt) REVERT: D 443 ASP cc_start: 0.7579 (m-30) cc_final: 0.7265 (m-30) outliers start: 19 outliers final: 9 residues processed: 234 average time/residue: 1.4110 time to fit residues: 364.3869 Evaluate side-chains 224 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 291 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 140 optimal weight: 0.0470 chunk 22 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 chunk 63 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN B 186 HIS ** B 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN C 186 HIS ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN D 186 HIS ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.177694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143759 restraints weight = 18513.667| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.51 r_work: 0.3572 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16716 Z= 0.353 Angle : 0.634 6.707 22696 Z= 0.333 Chirality : 0.047 0.141 2416 Planarity : 0.005 0.049 2892 Dihedral : 15.073 105.899 2724 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.34 % Allowed : 17.58 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.29 (0.19), residues: 1944 helix: 0.08 (0.20), residues: 716 sheet: -0.83 (0.26), residues: 380 loop : 0.12 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 462 HIS 0.004 0.001 HIS C 451 PHE 0.023 0.002 PHE B 56 TYR 0.025 0.003 TYR A 202 ARG 0.008 0.001 ARG A 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6320.99 seconds wall clock time: 113 minutes 9.09 seconds (6789.09 seconds total)