Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 22:36:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2023/7aho_11789_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2023/7aho_11789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2023/7aho_11789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2023/7aho_11789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2023/7aho_11789_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2023/7aho_11789_updated.pdb" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 6 5.49 5 S 69 5.16 5 C 8482 2.51 5 N 2355 2.21 5 O 2609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ASP 219": "OD1" <-> "OD2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "F ASP 234": "OD1" <-> "OD2" Residue "F ASP 264": "OD1" <-> "OD2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F GLU 351": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13521 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2338 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 2 Chain: "B" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2284 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2340 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2185 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2115 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2178 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.76, per 1000 atoms: 0.50 Number of scatterers: 13521 At special positions: 0 Unit cell: (73.29, 126.687, 131.922, 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 69 16.00 P 6 15.00 O 2609 8.00 N 2355 7.00 C 8482 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.0 seconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 17 sheets defined 42.3% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.537A pdb=" N GLU A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.580A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 199 removed outlier: 4.136A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.724A pdb=" N TYR A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.902A pdb=" N ASP A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 268' Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.852A pdb=" N ILE A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.721A pdb=" N HIS A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 331 removed outlier: 3.560A pdb=" N GLN A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 4.181A pdb=" N ILE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.107A pdb=" N GLU A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.031A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 5.018A pdb=" N SER B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.520A pdb=" N ALA B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 122 through 132 removed outlier: 4.034A pdb=" N ASN B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.646A pdb=" N VAL B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.731A pdb=" N THR B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 263 through 268 removed outlier: 5.261A pdb=" N ARG B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 removed outlier: 3.574A pdb=" N GLN B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.616A pdb=" N HIS B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 331 removed outlier: 4.388A pdb=" N LEU B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Proline residue: B 323 - end of helix removed outlier: 3.599A pdb=" N LEU B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.543A pdb=" N GLU B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 360 removed outlier: 3.932A pdb=" N LEU B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.218A pdb=" N SER C 31 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N HIS C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 27 through 32' Processing helix chain 'C' and resid 57 through 71 removed outlier: 4.086A pdb=" N GLU C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 100 removed outlier: 3.605A pdb=" N ALA C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 122 through 133 removed outlier: 3.612A pdb=" N ALA C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.868A pdb=" N LYS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 220 through 227 removed outlier: 3.632A pdb=" N THR C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 260 No H-bonds generated for 'chain 'C' and resid 258 through 260' Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.901A pdb=" N ILE C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 No H-bonds generated for 'chain 'C' and resid 302 through 305' Processing helix chain 'C' and resid 315 through 331 removed outlier: 3.969A pdb=" N GLN C 319 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Proline residue: C 323 - end of helix Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.958A pdb=" N GLU C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 344 " --> pdb=" O HIS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 357 through 360 No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.836A pdb=" N ALA D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 109 removed outlier: 3.622A pdb=" N ALA D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU D 109 " --> pdb=" O MET D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 130 through 139 removed outlier: 4.073A pdb=" N THR D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 139 " --> pdb=" O THR D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 165 No H-bonds generated for 'chain 'D' and resid 162 through 165' Processing helix chain 'D' and resid 190 through 201 removed outlier: 4.913A pdb=" N GLU D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 218 No H-bonds generated for 'chain 'D' and resid 216 through 218' Processing helix chain 'D' and resid 221 through 232 removed outlier: 3.556A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.785A pdb=" N LYS D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 311 removed outlier: 3.886A pdb=" N VAL D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.501A pdb=" N ALA D 323 " --> pdb=" O GLN D 319 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 359 removed outlier: 3.605A pdb=" N MET D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.762A pdb=" N ALA E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 77 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.508A pdb=" N GLN E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 195 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 216 through 218 No H-bonds generated for 'chain 'E' and resid 216 through 218' Processing helix chain 'E' and resid 221 through 224 No H-bonds generated for 'chain 'E' and resid 221 through 224' Processing helix chain 'E' and resid 226 through 232 removed outlier: 3.750A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU E 232 " --> pdb=" O ASN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 265 No H-bonds generated for 'chain 'E' and resid 263 through 265' Processing helix chain 'E' and resid 279 through 293 removed outlier: 3.681A pdb=" N GLN E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.803A pdb=" N ARG E 307 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 331 removed outlier: 3.976A pdb=" N ILE E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 323 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 4.064A pdb=" N LYS E 342 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 360 No H-bonds generated for 'chain 'E' and resid 357 through 360' Processing helix chain 'F' and resid 65 through 79 removed outlier: 3.733A pdb=" N ARG F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 107 No H-bonds generated for 'chain 'F' and resid 104 through 107' Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 160 through 165 removed outlier: 3.518A pdb=" N VAL F 164 " --> pdb=" O HIS F 160 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 165 " --> pdb=" O GLU F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 165' Processing helix chain 'F' and resid 188 through 201 removed outlier: 3.568A pdb=" N ASN F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA F 196 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 218 No H-bonds generated for 'chain 'F' and resid 216 through 218' Processing helix chain 'F' and resid 221 through 227 removed outlier: 5.373A pdb=" N PHE F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU F 227 " --> pdb=" O SER F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 260 No H-bonds generated for 'chain 'F' and resid 258 through 260' Processing helix chain 'F' and resid 266 through 268 No H-bonds generated for 'chain 'F' and resid 266 through 268' Processing helix chain 'F' and resid 279 through 289 removed outlier: 4.065A pdb=" N LYS F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE F 285 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 309 Processing helix chain 'F' and resid 314 through 319 Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.529A pdb=" N LEU F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 347 removed outlier: 3.815A pdb=" N VAL F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.697A pdb=" N MET F 358 " --> pdb=" O SER F 354 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS F 359 " --> pdb=" O THR F 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 354 through 359' Processing sheet with id= A, first strand: chain 'A' and resid 79 through 82 removed outlier: 3.612A pdb=" N LEU A 81 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.049A pdb=" N VAL A 209 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N MET A 110 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE A 211 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A 237 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL A 212 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 239 " --> pdb=" O VAL A 212 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 134 through 137 Processing sheet with id= D, first strand: chain 'B' and resid 269 through 271 removed outlier: 7.122A pdb=" N ALA B 79 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 242 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= F, first strand: chain 'B' and resid 246 through 248 Processing sheet with id= G, first strand: chain 'C' and resid 269 through 274 removed outlier: 7.043A pdb=" N ALA C 79 " --> pdb=" O MET C 270 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE C 272 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 81 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR C 274 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA C 83 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 135 through 138 Processing sheet with id= I, first strand: chain 'C' and resid 246 through 248 removed outlier: 3.650A pdb=" N SER C 257 " --> pdb=" O CYS C 247 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 87 through 90 Processing sheet with id= K, first strand: chain 'D' and resid 115 through 119 removed outlier: 8.248A pdb=" N VAL D 210 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ILE D 118 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE D 212 " --> pdb=" O ILE D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 247 through 249 Processing sheet with id= M, first strand: chain 'E' and resid 269 through 272 removed outlier: 6.703A pdb=" N ALA E 87 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL E 272 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU E 89 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP E 214 " --> pdb=" O ILE E 118 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 247 through 249 Processing sheet with id= O, first strand: chain 'F' and resid 269 through 273 removed outlier: 7.015A pdb=" N ALA F 87 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL F 272 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU F 89 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F 242 " --> pdb=" O ILE F 213 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR F 116 " --> pdb=" O VAL F 210 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 143 through 145 removed outlier: 3.557A pdb=" N GLY F 143 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 247 through 249 324 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4540 1.34 - 1.46: 2102 1.46 - 1.57: 6911 1.57 - 1.69: 9 1.69 - 1.81: 120 Bond restraints: 13682 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.460 0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C THR C 322 " pdb=" N PRO C 323 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.24e+00 bond pdb=" C GLY D 95 " pdb=" N THR D 96 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.24e+00 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.79e+00 ... (remaining 13677 not shown) Histogram of bond angle deviations from ideal: 97.44 - 105.03: 231 105.03 - 112.62: 7269 112.62 - 120.22: 5814 120.22 - 127.81: 5075 127.81 - 135.40: 78 Bond angle restraints: 18467 Sorted by residual: angle pdb=" C GLY F 333 " pdb=" N THR F 334 " pdb=" CA THR F 334 " ideal model delta sigma weight residual 121.54 132.97 -11.43 1.91e+00 2.74e-01 3.58e+01 angle pdb=" N GLN E 93 " pdb=" CA GLN E 93 " pdb=" C GLN E 93 " ideal model delta sigma weight residual 110.13 104.28 5.85 1.15e+00 7.56e-01 2.59e+01 angle pdb=" C ARG D 331 " pdb=" N LYS D 332 " pdb=" CA LYS D 332 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C GLU F 293 " pdb=" N ASP F 294 " pdb=" CA ASP F 294 " ideal model delta sigma weight residual 121.54 130.73 -9.19 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C GLY D 333 " pdb=" N THR D 334 " pdb=" CA THR D 334 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 ... (remaining 18462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.88: 8042 27.88 - 55.77: 350 55.77 - 83.65: 34 83.65 - 111.54: 5 111.54 - 139.42: 3 Dihedral angle restraints: 8434 sinusoidal: 3419 harmonic: 5015 Sorted by residual: dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual 300.00 160.58 139.42 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 66.40 -126.40 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 57.96 -117.95 1 2.00e+01 2.50e-03 3.53e+01 ... (remaining 8431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1648 0.060 - 0.120: 451 0.120 - 0.180: 82 0.180 - 0.240: 17 0.240 - 0.300: 2 Chirality restraints: 2200 Sorted by residual: chirality pdb=" CB ILE F 247 " pdb=" CA ILE F 247 " pdb=" CG1 ILE F 247 " pdb=" CG2 ILE F 247 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR C 313 " pdb=" CA THR C 313 " pdb=" OG1 THR C 313 " pdb=" CG2 THR C 313 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB VAL C 215 " pdb=" CA VAL C 215 " pdb=" CG1 VAL C 215 " pdb=" CG2 VAL C 215 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2197 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 322 " 0.046 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 323 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 257 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO B 258 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 278 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO B 279 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 279 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 279 " -0.034 5.00e-02 4.00e+02 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3363 2.78 - 3.31: 12301 3.31 - 3.84: 21581 3.84 - 4.37: 26134 4.37 - 4.90: 42097 Nonbonded interactions: 105476 Sorted by model distance: nonbonded pdb=" OG SER C 117 " pdb=" O ILE C 120 " model vdw 2.254 2.440 nonbonded pdb=" OG SER E 257 " pdb=" O ILE E 261 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR B 88 " pdb=" O MET B 275 " model vdw 2.270 2.440 nonbonded pdb=" O THR D 131 " pdb=" OG1 THR D 135 " model vdw 2.274 2.440 nonbonded pdb=" OH TYR C 116 " pdb=" O MET C 217 " model vdw 2.277 2.440 ... (remaining 105471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 138 or resid 147 through 155 or resid 188 throu \ gh 362 or resid 501)) selection = (chain 'B' and (resid 26 through 362 or resid 501)) selection = (chain 'C' and (resid 26 through 138 or resid 147 through 155 or resid 188 throu \ gh 362 or resid 501)) } ncs_group { reference = (chain 'D' and (resid 61 through 164 or resid 188 through 363)) selection = (chain 'E' and (resid 61 through 146 or resid 157 through 363)) selection = (chain 'F' and (resid 61 through 146 or resid 157 through 164 or resid 188 throu \ gh 363)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 5.810 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 34.690 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 0.060 13682 Z= 0.397 Angle : 0.921 11.431 18467 Z= 0.506 Chirality : 0.058 0.300 2200 Planarity : 0.006 0.068 2352 Dihedral : 15.599 139.419 5188 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.45 (0.15), residues: 1712 helix: -4.50 (0.08), residues: 821 sheet: -2.84 (0.32), residues: 219 loop : -2.33 (0.21), residues: 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 385 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 388 average time/residue: 0.3181 time to fit residues: 169.0990 Evaluate side-chains 261 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1160 time to fit residues: 2.4321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0980 chunk 130 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 156 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 325 ASN A 340 HIS B 56 GLN B 191 ASN C 34 HIS C 99 GLN C 227 HIS C 304 HIS D 64 GLN D 107 GLN D 217 HIS D 319 GLN D 337 GLN D 362 GLN E 64 GLN E 160 HIS ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 13682 Z= 0.162 Angle : 0.608 6.795 18467 Z= 0.309 Chirality : 0.044 0.165 2200 Planarity : 0.004 0.048 2352 Dihedral : 8.211 113.122 1908 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.17), residues: 1712 helix: -3.52 (0.12), residues: 852 sheet: -2.50 (0.31), residues: 227 loop : -1.87 (0.23), residues: 633 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 365 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 369 average time/residue: 0.2437 time to fit residues: 131.4076 Evaluate side-chains 257 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.0980 chunk 48 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 139 optimal weight: 0.0270 chunk 155 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN C 304 HIS D 160 HIS D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13682 Z= 0.140 Angle : 0.576 7.059 18467 Z= 0.288 Chirality : 0.043 0.195 2200 Planarity : 0.004 0.064 2352 Dihedral : 7.003 94.863 1908 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.18), residues: 1712 helix: -2.76 (0.14), residues: 850 sheet: -2.08 (0.33), residues: 220 loop : -1.54 (0.23), residues: 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.2472 time to fit residues: 135.1476 Evaluate side-chains 268 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 304 HIS C 319 GLN ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 160 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13682 Z= 0.232 Angle : 0.630 6.929 18467 Z= 0.309 Chirality : 0.046 0.535 2200 Planarity : 0.004 0.056 2352 Dihedral : 6.961 91.151 1908 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.18), residues: 1712 helix: -2.30 (0.15), residues: 858 sheet: -2.07 (0.33), residues: 211 loop : -1.40 (0.23), residues: 643 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 329 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 330 average time/residue: 0.2503 time to fit residues: 119.5392 Evaluate side-chains 253 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1600 time to fit residues: 2.4015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 136 GLN F 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13682 Z= 0.226 Angle : 0.621 7.939 18467 Z= 0.306 Chirality : 0.046 0.492 2200 Planarity : 0.004 0.041 2352 Dihedral : 6.683 92.798 1908 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.19), residues: 1712 helix: -2.02 (0.16), residues: 850 sheet: -2.19 (0.32), residues: 224 loop : -1.19 (0.24), residues: 638 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.2434 time to fit residues: 117.1098 Evaluate side-chains 253 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 166 optimal weight: 0.0050 chunk 138 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS D 136 GLN D 217 HIS ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN F 136 GLN F 160 HIS F 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 13682 Z= 0.154 Angle : 0.578 8.527 18467 Z= 0.282 Chirality : 0.045 0.519 2200 Planarity : 0.003 0.037 2352 Dihedral : 6.271 96.825 1908 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.19), residues: 1712 helix: -1.69 (0.17), residues: 836 sheet: -1.98 (0.33), residues: 219 loop : -1.04 (0.24), residues: 657 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 334 time to evaluate : 1.558 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.2284 time to fit residues: 114.2011 Evaluate side-chains 257 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 0.0970 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 340 HIS B 56 GLN C 227 HIS D 217 HIS D 259 HIS ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13682 Z= 0.257 Angle : 0.644 8.811 18467 Z= 0.318 Chirality : 0.047 0.555 2200 Planarity : 0.004 0.037 2352 Dihedral : 6.316 100.577 1908 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.19), residues: 1712 helix: -1.65 (0.17), residues: 848 sheet: -2.05 (0.32), residues: 225 loop : -1.06 (0.25), residues: 639 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 307 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.2440 time to fit residues: 110.8255 Evaluate side-chains 243 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 0.0060 chunk 158 optimal weight: 0.8980 chunk 144 optimal weight: 0.3980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 304 HIS D 136 GLN D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN F 160 HIS F 228 ASN ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 13682 Z= 0.144 Angle : 0.591 9.733 18467 Z= 0.290 Chirality : 0.045 0.564 2200 Planarity : 0.003 0.037 2352 Dihedral : 5.961 100.436 1908 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.20), residues: 1712 helix: -1.43 (0.17), residues: 851 sheet: -1.92 (0.33), residues: 226 loop : -0.93 (0.25), residues: 635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2407 time to fit residues: 117.9769 Evaluate side-chains 256 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 158 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 121 optimal weight: 0.0370 chunk 47 optimal weight: 0.6980 chunk 139 optimal weight: 0.0170 chunk 146 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 340 HIS B 56 GLN C 56 GLN C 227 HIS D 136 GLN D 217 HIS ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 13682 Z= 0.145 Angle : 0.589 9.762 18467 Z= 0.288 Chirality : 0.045 0.544 2200 Planarity : 0.003 0.037 2352 Dihedral : 5.786 99.798 1908 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.20), residues: 1712 helix: -1.24 (0.17), residues: 840 sheet: -1.74 (0.34), residues: 218 loop : -0.76 (0.25), residues: 654 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.2333 time to fit residues: 111.6568 Evaluate side-chains 258 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 105 optimal weight: 6.9990 chunk 83 optimal weight: 0.0040 chunk 108 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 overall best weight: 1.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS B 56 GLN B 340 HIS D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 13682 Z= 0.223 Angle : 0.635 10.671 18467 Z= 0.311 Chirality : 0.047 0.633 2200 Planarity : 0.003 0.035 2352 Dihedral : 5.926 100.390 1908 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.20), residues: 1712 helix: -1.21 (0.17), residues: 846 sheet: -1.75 (0.33), residues: 229 loop : -0.74 (0.25), residues: 637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2303 time to fit residues: 107.9111 Evaluate side-chains 246 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 5.9990 chunk 125 optimal weight: 0.0020 chunk 20 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN D 136 GLN D 190 GLN D 217 HIS D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100506 restraints weight = 27668.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102928 restraints weight = 16672.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104623 restraints weight = 11252.838| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13682 Z= 0.151 Angle : 0.600 9.952 18467 Z= 0.292 Chirality : 0.045 0.559 2200 Planarity : 0.003 0.037 2352 Dihedral : 5.742 98.081 1908 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.20), residues: 1712 helix: -1.10 (0.17), residues: 849 sheet: -1.67 (0.33), residues: 233 loop : -0.66 (0.25), residues: 630 =============================================================================== Job complete usr+sys time: 2960.18 seconds wall clock time: 54 minutes 24.28 seconds (3264.28 seconds total)