Starting phenix.real_space_refine on Mon Apr 8 12:57:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2024/7aho_11789_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2024/7aho_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_2024/7aho_11789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2024/7aho_11789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2024/7aho_11789_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aho_11789/04_2024/7aho_11789_updated.pdb" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.53, per 1000 atoms: 0.56 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: 5.46 Conformation dependent library (CDL) restraints added in 2.3 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: 2.65 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: 3.42 Time building geometry restraints manager: 5.85 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: 0.890 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: 5.190 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 37.720 Find NCS groups from input model: 1.020 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.090 ------------------------------------------------------------------------------- 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 % Allowed : 9.62 % Favored : 90.18 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 198 HIS 0.009 0.002 HIS A 152 PHE 0.028 0.002 PHE C 223 TYR 0.021 0.002 TYR E 345 ARG 0.012 0.001 ARG B 273 *********************** 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 : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.6893 (tm-30) cc_final: 0.6576 (tm-30) REVERT: A 81 LEU cc_start: 0.8881 (tt) cc_final: 0.8667 (tt) REVERT: A 114 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7630 (tp30) REVERT: A 227 HIS cc_start: 0.8271 (t-90) cc_final: 0.8001 (t-170) REVERT: A 282 MET cc_start: 0.8031 (mmt) cc_final: 0.7498 (mmt) REVERT: A 295 ILE cc_start: 0.9081 (mm) cc_final: 0.8826 (mm) REVERT: A 303 ASN cc_start: 0.7654 (m-40) cc_final: 0.7405 (m110) REVERT: B 121 LYS cc_start: 0.7856 (ptmt) cc_final: 0.7023 (mttm) REVERT: B 196 LYS cc_start: 0.8697 (tttt) cc_final: 0.8463 (tttp) REVERT: B 197 TYR cc_start: 0.6403 (m-10) cc_final: 0.5657 (m-80) REVERT: B 338 LYS cc_start: 0.8276 (tttt) cc_final: 0.8043 (tttt) REVERT: C 58 ASN cc_start: 0.8600 (t0) cc_final: 0.8244 (t0) REVERT: C 69 LEU cc_start: 0.9273 (mp) cc_final: 0.9055 (mp) REVERT: C 91 THR cc_start: 0.8686 (m) cc_final: 0.8269 (p) REVERT: C 131 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7394 (mtp-110) REVERT: C 134 ILE cc_start: 0.8679 (mt) cc_final: 0.8453 (mm) REVERT: C 225 TYR cc_start: 0.8553 (t80) cc_final: 0.8205 (t80) REVERT: C 319 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7366 (tm-30) REVERT: C 350 ASP cc_start: 0.8139 (p0) cc_final: 0.7781 (p0) REVERT: D 140 ARG cc_start: 0.8351 (ttm170) cc_final: 0.8147 (ptp-170) REVERT: D 308 ILE cc_start: 0.8956 (mm) cc_final: 0.8160 (mm) REVERT: E 128 MET cc_start: 0.3750 (ptp) cc_final: 0.3034 (pmm) REVERT: E 139 ARG cc_start: 0.5826 (mtm-85) cc_final: 0.5586 (mmt90) REVERT: E 140 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7949 (mtp180) REVERT: E 161 GLU cc_start: 0.6135 (mt-10) cc_final: 0.5926 (mp0) REVERT: E 199 ARG cc_start: 0.6306 (mtm180) cc_final: 0.5177 (tmm160) REVERT: E 203 LYS cc_start: 0.4244 (mmtt) cc_final: 0.2500 (tptm) REVERT: E 221 ILE cc_start: 0.9162 (tp) cc_final: 0.8800 (tp) REVERT: E 225 SER cc_start: 0.8842 (t) cc_final: 0.8547 (t) REVERT: E 316 TYR cc_start: 0.8591 (t80) cc_final: 0.8347 (t80) REVERT: E 319 GLN cc_start: 0.7671 (mt0) cc_final: 0.6910 (mm-40) REVERT: E 330 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8452 (mtpt) REVERT: F 68 ARG cc_start: 0.7004 (mtp180) cc_final: 0.6708 (mtp-110) REVERT: F 75 LEU cc_start: 0.8811 (mt) cc_final: 0.8260 (mt) REVERT: F 82 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7854 (mttm) REVERT: F 220 ASP cc_start: 0.8093 (p0) cc_final: 0.7751 (m-30) REVERT: F 228 ASN cc_start: 0.7621 (t0) cc_final: 0.7336 (t0) REVERT: F 319 GLN cc_start: 0.8756 (mt0) cc_final: 0.7806 (tt0) outliers start: 3 outliers final: 1 residues processed: 388 average time/residue: 0.2970 time to fit residues: 158.4590 Evaluate side-chains 277 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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: 0.7980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 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: 0.9782 ------------------------------------------------------------------------------- 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 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 160 HIS 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 F 319 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13682 Z= 0.207 Angle : 0.620 6.626 18467 Z= 0.317 Chirality : 0.044 0.165 2200 Planarity : 0.005 0.048 2352 Dihedral : 8.540 119.342 1908 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.21 % Allowed : 6.11 % Favored : 93.68 % 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: -4.44 (0.17), residues: 1712 helix: -3.53 (0.12), residues: 838 sheet: -2.68 (0.31), residues: 216 loop : -1.85 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 198 HIS 0.005 0.001 HIS A 152 PHE 0.014 0.001 PHE D 115 TYR 0.016 0.002 TYR E 345 ARG 0.003 0.000 ARG E 289 *********************** 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 346 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 343 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8781 (m) cc_final: 0.8436 (m) REVERT: A 114 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7445 (tp30) REVERT: A 227 HIS cc_start: 0.8270 (t-90) cc_final: 0.7980 (t-170) REVERT: A 282 MET cc_start: 0.8015 (mmt) cc_final: 0.7429 (mmt) REVERT: A 303 ASN cc_start: 0.7809 (m-40) cc_final: 0.7513 (m-40) REVERT: B 121 LYS cc_start: 0.7792 (ptmt) cc_final: 0.6999 (mttm) REVERT: B 127 MET cc_start: 0.8801 (mmm) cc_final: 0.8516 (mmp) REVERT: B 197 TYR cc_start: 0.6508 (m-10) cc_final: 0.5679 (m-80) REVERT: B 217 MET cc_start: 0.7394 (tpp) cc_final: 0.7093 (tpp) REVERT: B 271 ILE cc_start: 0.8797 (mp) cc_final: 0.8523 (mt) REVERT: B 295 ILE cc_start: 0.8246 (pt) cc_final: 0.8019 (mm) REVERT: C 58 ASN cc_start: 0.8853 (t0) cc_final: 0.8401 (t0) REVERT: C 134 ILE cc_start: 0.8531 (mt) cc_final: 0.8193 (mm) REVERT: C 197 TYR cc_start: 0.7411 (m-80) cc_final: 0.7171 (m-80) REVERT: C 225 TYR cc_start: 0.8773 (t80) cc_final: 0.8398 (t80) REVERT: C 319 GLN cc_start: 0.8342 (mm-40) cc_final: 0.7451 (tm-30) REVERT: C 323 PRO cc_start: 0.9271 (Cg_exo) cc_final: 0.9040 (Cg_endo) REVERT: C 350 ASP cc_start: 0.8147 (p0) cc_final: 0.7698 (p0) REVERT: D 140 ARG cc_start: 0.8328 (ttm170) cc_final: 0.7778 (ttm110) REVERT: D 217 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.7073 (p90) REVERT: D 308 ILE cc_start: 0.8879 (mm) cc_final: 0.8340 (mm) REVERT: E 128 MET cc_start: 0.3830 (ptp) cc_final: 0.3208 (pmm) REVERT: E 140 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7991 (mtp180) REVERT: E 199 ARG cc_start: 0.6185 (mtm180) cc_final: 0.5108 (tmm160) REVERT: E 203 LYS cc_start: 0.3868 (mmtt) cc_final: 0.2270 (tptm) REVERT: E 319 GLN cc_start: 0.7739 (mt0) cc_final: 0.6954 (mm-40) REVERT: E 330 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8262 (mtpt) REVERT: F 68 ARG cc_start: 0.7037 (mtp180) cc_final: 0.6751 (mtp-110) REVERT: F 77 MET cc_start: 0.9270 (ttp) cc_final: 0.8838 (ttm) REVERT: F 82 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7733 (mttm) REVERT: F 105 MET cc_start: 0.8101 (mmp) cc_final: 0.7456 (mmt) REVERT: F 107 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6242 (mp10) REVERT: F 158 SER cc_start: 0.7817 (m) cc_final: 0.7592 (t) REVERT: F 220 ASP cc_start: 0.8241 (p0) cc_final: 0.7643 (m-30) REVERT: F 315 ARG cc_start: 0.7120 (ttp80) cc_final: 0.6907 (ptt90) outliers start: 3 outliers final: 0 residues processed: 346 average time/residue: 0.2664 time to fit residues: 132.4951 Evaluate side-chains 268 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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: 0.8980 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 304 HIS B 56 GLN C 304 HIS D 166 ASN D 319 GLN ** E 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13682 Z= 0.247 Angle : 0.630 7.632 18467 Z= 0.317 Chirality : 0.045 0.206 2200 Planarity : 0.004 0.037 2352 Dihedral : 8.031 112.223 1908 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: -3.61 (0.18), residues: 1712 helix: -2.77 (0.14), residues: 835 sheet: -2.51 (0.32), residues: 215 loop : -1.48 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 198 HIS 0.005 0.001 HIS A 152 PHE 0.024 0.002 PHE B 223 TYR 0.021 0.002 TYR A 197 ARG 0.009 0.000 ARG B 268 *********************** 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 329 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8654 (m) cc_final: 0.8397 (m) REVERT: A 114 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7324 (tp30) REVERT: A 127 MET cc_start: 0.6958 (ttt) cc_final: 0.6755 (ttt) REVERT: A 227 HIS cc_start: 0.8340 (t-90) cc_final: 0.8024 (t-170) REVERT: A 282 MET cc_start: 0.8057 (mmt) cc_final: 0.7393 (mmt) REVERT: A 303 ASN cc_start: 0.7647 (m-40) cc_final: 0.7356 (m-40) REVERT: B 121 LYS cc_start: 0.7904 (ptmt) cc_final: 0.7127 (mttm) REVERT: B 127 MET cc_start: 0.8768 (mmm) cc_final: 0.8552 (mmp) REVERT: B 197 TYR cc_start: 0.6584 (m-10) cc_final: 0.5666 (m-80) REVERT: B 217 MET cc_start: 0.7503 (tpp) cc_final: 0.7231 (tpp) REVERT: B 231 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6953 (tt0) REVERT: B 271 ILE cc_start: 0.8809 (mp) cc_final: 0.8574 (mt) REVERT: B 338 LYS cc_start: 0.8126 (tttt) cc_final: 0.7765 (mttt) REVERT: C 58 ASN cc_start: 0.8813 (t0) cc_final: 0.8395 (t0) REVERT: C 108 CYS cc_start: 0.7601 (p) cc_final: 0.7306 (t) REVERT: C 225 TYR cc_start: 0.8817 (t80) cc_final: 0.8448 (t80) REVERT: C 319 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7375 (tm-30) REVERT: C 323 PRO cc_start: 0.9275 (Cg_exo) cc_final: 0.9069 (Cg_endo) REVERT: C 338 LYS cc_start: 0.7605 (tptp) cc_final: 0.7272 (tppt) REVERT: C 350 ASP cc_start: 0.8136 (p0) cc_final: 0.7717 (p0) REVERT: D 140 ARG cc_start: 0.8429 (ttm170) cc_final: 0.7923 (ttm110) REVERT: D 280 LYS cc_start: 0.8709 (tttt) cc_final: 0.8440 (ttmm) REVERT: D 308 ILE cc_start: 0.8886 (mm) cc_final: 0.8494 (mm) REVERT: E 128 MET cc_start: 0.3816 (ptp) cc_final: 0.3218 (pmm) REVERT: E 132 GLU cc_start: 0.7964 (tp30) cc_final: 0.7688 (tp30) REVERT: E 140 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7973 (mtp180) REVERT: E 161 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5737 (mp0) REVERT: E 199 ARG cc_start: 0.6337 (mtm180) cc_final: 0.5257 (tmm160) REVERT: E 203 LYS cc_start: 0.3771 (mmtt) cc_final: 0.2323 (tppt) REVERT: E 211 LEU cc_start: 0.9016 (tp) cc_final: 0.8785 (tt) REVERT: E 330 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8155 (ttmt) REVERT: E 336 VAL cc_start: 0.7469 (t) cc_final: 0.7120 (t) REVERT: F 68 ARG cc_start: 0.7095 (mtp180) cc_final: 0.6765 (mmm160) REVERT: F 103 MET cc_start: 0.7999 (ptp) cc_final: 0.7424 (ppp) REVERT: F 105 MET cc_start: 0.8024 (mmp) cc_final: 0.6795 (ttt) REVERT: F 220 ASP cc_start: 0.8228 (p0) cc_final: 0.7762 (m-30) REVERT: F 361 TYR cc_start: 0.7277 (t80) cc_final: 0.7032 (t80) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2783 time to fit residues: 131.3025 Evaluate side-chains 251 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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: 1.9990 chunk 117 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 0.0070 chunk 105 optimal weight: 0.5980 chunk 157 optimal weight: 0.0980 chunk 166 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 304 HIS A 340 HIS B 56 GLN C 304 HIS D 217 HIS D 319 GLN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13682 Z= 0.155 Angle : 0.568 6.999 18467 Z= 0.283 Chirality : 0.043 0.159 2200 Planarity : 0.003 0.043 2352 Dihedral : 7.091 97.727 1908 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % 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: -3.05 (0.18), residues: 1712 helix: -2.20 (0.16), residues: 835 sheet: -2.22 (0.33), residues: 215 loop : -1.38 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 198 HIS 0.006 0.001 HIS C 304 PHE 0.011 0.001 PHE D 115 TYR 0.018 0.002 TYR A 197 ARG 0.005 0.000 ARG F 315 *********************** 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 339 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8663 (m) cc_final: 0.8461 (m) REVERT: A 114 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7139 (tp30) REVERT: A 227 HIS cc_start: 0.8371 (t-90) cc_final: 0.8040 (t-170) REVERT: A 275 MET cc_start: 0.7018 (mtm) cc_final: 0.6775 (mtm) REVERT: A 303 ASN cc_start: 0.7748 (m-40) cc_final: 0.7454 (m-40) REVERT: B 121 LYS cc_start: 0.7949 (ptmt) cc_final: 0.7208 (mttm) REVERT: B 127 MET cc_start: 0.8657 (mmm) cc_final: 0.8336 (mmp) REVERT: B 231 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6888 (tt0) REVERT: B 304 HIS cc_start: 0.6994 (t-170) cc_final: 0.6715 (t-170) REVERT: B 334 ASP cc_start: 0.7191 (m-30) cc_final: 0.6721 (p0) REVERT: B 338 LYS cc_start: 0.8148 (tttt) cc_final: 0.7607 (mttt) REVERT: C 58 ASN cc_start: 0.8787 (t0) cc_final: 0.8382 (t0) REVERT: C 108 CYS cc_start: 0.7700 (p) cc_final: 0.7385 (t) REVERT: C 192 LYS cc_start: 0.7376 (ttmt) cc_final: 0.7134 (tmtt) REVERT: C 225 TYR cc_start: 0.8792 (t80) cc_final: 0.8441 (t80) REVERT: C 307 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7186 (mt-10) REVERT: C 319 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7361 (tm-30) REVERT: C 323 PRO cc_start: 0.9275 (Cg_exo) cc_final: 0.9070 (Cg_endo) REVERT: C 350 ASP cc_start: 0.8034 (p0) cc_final: 0.7728 (p0) REVERT: D 140 ARG cc_start: 0.8380 (ttm170) cc_final: 0.7865 (ttm170) REVERT: D 228 ASN cc_start: 0.8313 (m-40) cc_final: 0.7864 (m-40) REVERT: D 308 ILE cc_start: 0.8727 (mm) cc_final: 0.8317 (mm) REVERT: E 105 MET cc_start: 0.8772 (mpp) cc_final: 0.8544 (mpp) REVERT: E 128 MET cc_start: 0.3790 (ptp) cc_final: 0.3215 (pmm) REVERT: E 140 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7956 (mtp180) REVERT: E 199 ARG cc_start: 0.6188 (mtm180) cc_final: 0.5266 (tmm160) REVERT: E 203 LYS cc_start: 0.3666 (mmtt) cc_final: 0.2185 (tptm) REVERT: E 211 LEU cc_start: 0.9049 (tp) cc_final: 0.8842 (tt) REVERT: E 221 ILE cc_start: 0.9095 (tp) cc_final: 0.8883 (tp) REVERT: E 327 VAL cc_start: 0.8689 (m) cc_final: 0.8328 (p) REVERT: E 330 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8291 (ttpt) REVERT: F 68 ARG cc_start: 0.7106 (mtp180) cc_final: 0.6770 (mmm160) REVERT: F 103 MET cc_start: 0.7810 (ptp) cc_final: 0.7421 (ppp) REVERT: F 158 SER cc_start: 0.7797 (m) cc_final: 0.7535 (t) REVERT: F 218 MET cc_start: 0.8876 (mmm) cc_final: 0.8647 (mmt) REVERT: F 220 ASP cc_start: 0.8242 (p0) cc_final: 0.7649 (m-30) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.2648 time to fit residues: 129.9965 Evaluate side-chains 261 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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: 3.9990 chunk 94 optimal weight: 0.3980 chunk 2 optimal weight: 0.0010 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 0.0050 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS C 304 HIS D 217 HIS D 319 GLN F 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13682 Z= 0.147 Angle : 0.557 6.878 18467 Z= 0.274 Chirality : 0.043 0.162 2200 Planarity : 0.003 0.045 2352 Dihedral : 6.554 91.482 1908 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % 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: -2.57 (0.19), residues: 1712 helix: -1.80 (0.17), residues: 827 sheet: -2.04 (0.32), residues: 224 loop : -1.12 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 198 HIS 0.004 0.001 HIS A 152 PHE 0.010 0.001 PHE F 365 TYR 0.017 0.001 TYR A 197 ARG 0.004 0.000 ARG E 188 *********************** 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 344 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8846 (m) cc_final: 0.8610 (m) REVERT: A 114 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7018 (tp30) REVERT: A 127 MET cc_start: 0.7086 (ttt) cc_final: 0.6883 (ttm) REVERT: A 227 HIS cc_start: 0.8317 (t-90) cc_final: 0.7991 (t-170) REVERT: A 303 ASN cc_start: 0.7792 (m-40) cc_final: 0.7473 (m-40) REVERT: B 121 LYS cc_start: 0.7999 (ptmt) cc_final: 0.7318 (mttm) REVERT: B 127 MET cc_start: 0.8515 (mmm) cc_final: 0.8289 (mmp) REVERT: B 231 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6856 (tt0) REVERT: B 275 MET cc_start: 0.8042 (mmm) cc_final: 0.7785 (mmm) REVERT: B 304 HIS cc_start: 0.6924 (t-170) cc_final: 0.6533 (t-90) REVERT: B 316 TYR cc_start: 0.7604 (t80) cc_final: 0.7218 (t80) REVERT: B 334 ASP cc_start: 0.7273 (m-30) cc_final: 0.6836 (p0) REVERT: B 338 LYS cc_start: 0.8068 (tttt) cc_final: 0.7661 (mttt) REVERT: B 342 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6863 (pt0) REVERT: C 58 ASN cc_start: 0.8781 (t0) cc_final: 0.8360 (t0) REVERT: C 192 LYS cc_start: 0.7244 (ttmt) cc_final: 0.7014 (tmtt) REVERT: C 217 MET cc_start: 0.8115 (mmm) cc_final: 0.7753 (mtp) REVERT: C 225 TYR cc_start: 0.8832 (t80) cc_final: 0.8509 (t80) REVERT: C 254 ASP cc_start: 0.8323 (t0) cc_final: 0.7874 (t0) REVERT: C 319 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8070 (mp10) REVERT: C 350 ASP cc_start: 0.7989 (p0) cc_final: 0.7772 (p0) REVERT: D 105 MET cc_start: 0.8336 (tpp) cc_final: 0.8119 (tpp) REVERT: D 140 ARG cc_start: 0.8375 (ttm170) cc_final: 0.7904 (ttm170) REVERT: D 217 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.7025 (p90) REVERT: D 228 ASN cc_start: 0.8132 (m-40) cc_final: 0.7626 (m-40) REVERT: D 308 ILE cc_start: 0.8668 (mm) cc_final: 0.8256 (mm) REVERT: E 128 MET cc_start: 0.3667 (ptp) cc_final: 0.3123 (pmm) REVERT: E 199 ARG cc_start: 0.6131 (mtm180) cc_final: 0.5293 (ttp80) REVERT: E 203 LYS cc_start: 0.3571 (mmtt) cc_final: 0.2072 (tptm) REVERT: E 223 SER cc_start: 0.8547 (m) cc_final: 0.8145 (t) REVERT: E 228 ASN cc_start: 0.8187 (t0) cc_final: 0.7713 (t0) REVERT: E 327 VAL cc_start: 0.8629 (m) cc_final: 0.8352 (p) REVERT: E 330 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8353 (ttpt) REVERT: F 68 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6859 (mmm160) REVERT: F 83 ILE cc_start: 0.8905 (tp) cc_final: 0.8679 (tp) REVERT: F 103 MET cc_start: 0.7650 (ptp) cc_final: 0.7310 (ppp) REVERT: F 105 MET cc_start: 0.7696 (mmp) cc_final: 0.6747 (tpp) REVERT: F 158 SER cc_start: 0.7825 (m) cc_final: 0.7546 (t) REVERT: F 218 MET cc_start: 0.8842 (mmm) cc_final: 0.8565 (mmt) REVERT: F 220 ASP cc_start: 0.8207 (p0) cc_final: 0.7682 (m-30) REVERT: F 315 ARG cc_start: 0.6903 (ptt90) cc_final: 0.6217 (ptt90) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.2555 time to fit residues: 128.5112 Evaluate side-chains 259 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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: 0.6980 chunk 149 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 160 optimal weight: 0.0270 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 304 HIS E 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3515 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= 0.140 Angle : 0.558 8.148 18467 Z= 0.272 Chirality : 0.043 0.227 2200 Planarity : 0.003 0.043 2352 Dihedral : 6.213 93.796 1908 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -2.34 (0.19), residues: 1712 helix: -1.58 (0.17), residues: 838 sheet: -1.89 (0.33), residues: 224 loop : -1.05 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 198 HIS 0.005 0.001 HIS A 152 PHE 0.012 0.001 PHE E 348 TYR 0.013 0.001 TYR F 361 ARG 0.006 0.000 ARG A 250 *********************** 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: 0 poor density : 335 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8858 (m) cc_final: 0.8616 (m) REVERT: A 114 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6967 (tp30) REVERT: A 127 MET cc_start: 0.7232 (ttt) cc_final: 0.6924 (ttm) REVERT: A 295 ILE cc_start: 0.9364 (mp) cc_final: 0.8920 (mm) REVERT: A 303 ASN cc_start: 0.7844 (m-40) cc_final: 0.7532 (m-40) REVERT: B 121 LYS cc_start: 0.8009 (ptmt) cc_final: 0.7311 (mttm) REVERT: B 127 MET cc_start: 0.8458 (mmm) cc_final: 0.8256 (mmp) REVERT: B 304 HIS cc_start: 0.6952 (t-170) cc_final: 0.6552 (t-90) REVERT: B 316 TYR cc_start: 0.7505 (t80) cc_final: 0.7206 (t80) REVERT: B 334 ASP cc_start: 0.7263 (m-30) cc_final: 0.6826 (p0) REVERT: B 338 LYS cc_start: 0.8030 (tttt) cc_final: 0.7828 (mttt) REVERT: C 58 ASN cc_start: 0.8703 (t0) cc_final: 0.8242 (t0) REVERT: C 131 ARG cc_start: 0.8641 (mtt-85) cc_final: 0.8420 (mtt-85) REVERT: C 192 LYS cc_start: 0.7272 (ttmt) cc_final: 0.6895 (tmtt) REVERT: C 225 TYR cc_start: 0.8842 (t80) cc_final: 0.8530 (t80) REVERT: C 254 ASP cc_start: 0.7978 (t0) cc_final: 0.7707 (t0) REVERT: D 140 ARG cc_start: 0.8353 (ttm170) cc_final: 0.8078 (ttp-170) REVERT: D 228 ASN cc_start: 0.8075 (m-40) cc_final: 0.7563 (m-40) REVERT: D 308 ILE cc_start: 0.8570 (mm) cc_final: 0.8156 (mm) REVERT: E 128 MET cc_start: 0.3642 (ptp) cc_final: 0.3149 (pmm) REVERT: E 199 ARG cc_start: 0.6003 (mtm180) cc_final: 0.5135 (ttp80) REVERT: E 203 LYS cc_start: 0.3401 (mmtt) cc_final: 0.2292 (tptm) REVERT: E 221 ILE cc_start: 0.9127 (tp) cc_final: 0.8893 (tp) REVERT: E 223 SER cc_start: 0.8456 (m) cc_final: 0.8083 (t) REVERT: E 327 VAL cc_start: 0.8690 (m) cc_final: 0.8377 (p) REVERT: E 330 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8367 (ttpt) REVERT: F 103 MET cc_start: 0.7606 (ptp) cc_final: 0.7191 (ppp) REVERT: F 105 MET cc_start: 0.7671 (mmp) cc_final: 0.6764 (tpp) REVERT: F 128 MET cc_start: 0.7004 (mtm) cc_final: 0.6042 (mmp) REVERT: F 158 SER cc_start: 0.7848 (m) cc_final: 0.7558 (t) REVERT: F 220 ASP cc_start: 0.7996 (p0) cc_final: 0.7651 (m-30) REVERT: F 315 ARG cc_start: 0.6966 (ptt90) cc_final: 0.6282 (ptt90) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2672 time to fit residues: 132.4280 Evaluate side-chains 261 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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: 0.9980 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS D 217 HIS D 259 HIS F 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13682 Z= 0.172 Angle : 0.584 7.353 18467 Z= 0.286 Chirality : 0.043 0.191 2200 Planarity : 0.003 0.040 2352 Dihedral : 6.121 96.746 1908 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.14 % Allowed : 1.99 % Favored : 97.87 % 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: -2.05 (0.20), residues: 1712 helix: -1.39 (0.17), residues: 822 sheet: -1.93 (0.34), residues: 209 loop : -0.82 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 198 HIS 0.005 0.001 HIS A 152 PHE 0.016 0.001 PHE F 348 TYR 0.013 0.001 TYR F 361 ARG 0.006 0.000 ARG B 273 *********************** 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 323 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 321 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8850 (m) cc_final: 0.8612 (m) REVERT: A 114 GLU cc_start: 0.7599 (tm-30) cc_final: 0.6934 (tp30) REVERT: A 127 MET cc_start: 0.7246 (ttt) cc_final: 0.6929 (ttm) REVERT: A 295 ILE cc_start: 0.9376 (mp) cc_final: 0.9122 (mm) REVERT: A 303 ASN cc_start: 0.7752 (m-40) cc_final: 0.7492 (m-40) REVERT: B 121 LYS cc_start: 0.7965 (ptmt) cc_final: 0.7295 (mttm) REVERT: B 127 MET cc_start: 0.8459 (mmm) cc_final: 0.8258 (mmp) REVERT: B 267 ASP cc_start: 0.8810 (m-30) cc_final: 0.8573 (m-30) REVERT: B 304 HIS cc_start: 0.6814 (t-170) cc_final: 0.6497 (t-90) REVERT: B 316 TYR cc_start: 0.7522 (t80) cc_final: 0.7180 (t80) REVERT: B 334 ASP cc_start: 0.7144 (m-30) cc_final: 0.6888 (p0) REVERT: C 58 ASN cc_start: 0.8746 (t0) cc_final: 0.8278 (t0) REVERT: C 192 LYS cc_start: 0.7302 (ttmt) cc_final: 0.6923 (tmtt) REVERT: C 225 TYR cc_start: 0.8850 (t80) cc_final: 0.8528 (t80) REVERT: D 140 ARG cc_start: 0.8322 (ttm170) cc_final: 0.8071 (ttp-170) REVERT: D 217 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.7126 (p90) REVERT: D 228 ASN cc_start: 0.8074 (m-40) cc_final: 0.7633 (m-40) REVERT: D 308 ILE cc_start: 0.8703 (mm) cc_final: 0.8412 (mm) REVERT: E 128 MET cc_start: 0.3743 (ptp) cc_final: 0.3131 (pmm) REVERT: E 199 ARG cc_start: 0.6047 (mtm180) cc_final: 0.5103 (tmm160) REVERT: E 203 LYS cc_start: 0.3405 (mmtt) cc_final: 0.2354 (tptm) REVERT: E 223 SER cc_start: 0.8469 (m) cc_final: 0.8111 (t) REVERT: E 327 VAL cc_start: 0.8702 (m) cc_final: 0.8400 (p) REVERT: E 330 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8368 (ttpt) REVERT: E 345 TYR cc_start: 0.7778 (t80) cc_final: 0.7526 (t80) REVERT: F 128 MET cc_start: 0.7002 (mtm) cc_final: 0.6010 (mmp) REVERT: F 220 ASP cc_start: 0.8090 (p0) cc_final: 0.7715 (m-30) REVERT: F 315 ARG cc_start: 0.6949 (ptt90) cc_final: 0.6651 (ptm160) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.2504 time to fit residues: 119.4009 Evaluate side-chains 258 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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: 0.0060 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 150 optimal weight: 0.0970 chunk 158 optimal weight: 0.0370 chunk 144 optimal weight: 0.2980 overall best weight: 0.1272 ------------------------------------------------------------------------------- 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 D 319 GLN F 160 HIS F 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13682 Z= 0.128 Angle : 0.557 6.769 18467 Z= 0.273 Chirality : 0.042 0.174 2200 Planarity : 0.003 0.042 2352 Dihedral : 5.766 100.452 1908 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.20), residues: 1712 helix: -1.20 (0.17), residues: 837 sheet: -1.72 (0.34), residues: 215 loop : -0.73 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 198 HIS 0.006 0.001 HIS C 304 PHE 0.010 0.001 PHE A 223 TYR 0.016 0.001 TYR F 302 ARG 0.006 0.000 ARG C 315 *********************** 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 346 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8859 (m) cc_final: 0.8628 (m) REVERT: A 114 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6953 (tp30) REVERT: A 127 MET cc_start: 0.7360 (ttt) cc_final: 0.6957 (ttm) REVERT: A 234 ILE cc_start: 0.6183 (mp) cc_final: 0.5937 (mp) REVERT: A 295 ILE cc_start: 0.9371 (mp) cc_final: 0.9096 (mm) REVERT: B 121 LYS cc_start: 0.7911 (ptmt) cc_final: 0.7319 (mttm) REVERT: B 267 ASP cc_start: 0.8716 (m-30) cc_final: 0.8474 (m-30) REVERT: B 334 ASP cc_start: 0.7136 (m-30) cc_final: 0.6894 (p0) REVERT: C 58 ASN cc_start: 0.8680 (t0) cc_final: 0.8376 (t0) REVERT: C 132 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7424 (ttm170) REVERT: C 192 LYS cc_start: 0.7070 (ttmt) cc_final: 0.6699 (tmtt) REVERT: C 225 TYR cc_start: 0.8851 (t80) cc_final: 0.8514 (t80) REVERT: C 266 LEU cc_start: 0.8000 (tp) cc_final: 0.7700 (tp) REVERT: C 282 MET cc_start: 0.7316 (tpt) cc_final: 0.6864 (tpt) REVERT: D 132 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6605 (mm-30) REVERT: D 140 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7404 (ttm170) REVERT: D 228 ASN cc_start: 0.8064 (m-40) cc_final: 0.7530 (m-40) REVERT: D 308 ILE cc_start: 0.8680 (mm) cc_final: 0.8424 (mm) REVERT: E 128 MET cc_start: 0.3858 (ptp) cc_final: 0.3266 (pmm) REVERT: E 199 ARG cc_start: 0.6081 (mtm180) cc_final: 0.5091 (tmm160) REVERT: E 203 LYS cc_start: 0.3179 (mmtt) cc_final: 0.2070 (tptm) REVERT: E 223 SER cc_start: 0.8461 (m) cc_final: 0.8101 (t) REVERT: E 228 ASN cc_start: 0.7984 (t0) cc_final: 0.7617 (t0) REVERT: E 315 ARG cc_start: 0.8197 (ptt90) cc_final: 0.7929 (ptt90) REVERT: E 327 VAL cc_start: 0.8611 (m) cc_final: 0.8326 (p) REVERT: E 330 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8304 (ttmt) REVERT: E 345 TYR cc_start: 0.7732 (t80) cc_final: 0.7478 (t80) REVERT: F 105 MET cc_start: 0.7424 (mmp) cc_final: 0.6308 (tpp) REVERT: F 158 SER cc_start: 0.7867 (m) cc_final: 0.7593 (t) REVERT: F 220 ASP cc_start: 0.8074 (p0) cc_final: 0.7489 (m-30) REVERT: F 315 ARG cc_start: 0.6959 (ptt90) cc_final: 0.6699 (ptm160) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2554 time to fit residues: 128.7201 Evaluate side-chains 271 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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: 0.9990 chunk 158 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 0.1980 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** D 217 HIS D 319 GLN F 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13682 Z= 0.169 Angle : 0.581 7.636 18467 Z= 0.284 Chirality : 0.043 0.166 2200 Planarity : 0.003 0.040 2352 Dihedral : 5.727 100.627 1908 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1712 helix: -1.07 (0.18), residues: 848 sheet: -1.59 (0.35), residues: 209 loop : -0.73 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 198 HIS 0.005 0.001 HIS B 304 PHE 0.010 0.001 PHE F 348 TYR 0.014 0.001 TYR F 302 ARG 0.006 0.000 ARG B 273 *********************** 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 325 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8900 (m) cc_final: 0.8640 (m) REVERT: A 127 MET cc_start: 0.7547 (ttt) cc_final: 0.7258 (ttm) REVERT: A 295 ILE cc_start: 0.9401 (mp) cc_final: 0.9127 (mm) REVERT: B 121 LYS cc_start: 0.7915 (ptmt) cc_final: 0.7336 (mttm) REVERT: B 127 MET cc_start: 0.8788 (mmp) cc_final: 0.8241 (mmt) REVERT: B 334 ASP cc_start: 0.7232 (m-30) cc_final: 0.6912 (p0) REVERT: C 58 ASN cc_start: 0.8710 (t0) cc_final: 0.8402 (t0) REVERT: C 132 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7428 (ttm170) REVERT: C 192 LYS cc_start: 0.7198 (ttmt) cc_final: 0.6856 (tmtt) REVERT: C 225 TYR cc_start: 0.8884 (t80) cc_final: 0.8520 (t80) REVERT: C 282 MET cc_start: 0.7094 (tpt) cc_final: 0.6730 (tpt) REVERT: C 307 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6270 (mt-10) REVERT: D 140 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7980 (ttp-170) REVERT: D 228 ASN cc_start: 0.8121 (m-40) cc_final: 0.7581 (m-40) REVERT: D 288 ILE cc_start: 0.8304 (tp) cc_final: 0.8098 (tp) REVERT: D 308 ILE cc_start: 0.8704 (mm) cc_final: 0.8302 (mm) REVERT: E 128 MET cc_start: 0.4041 (ptp) cc_final: 0.3327 (pmm) REVERT: E 199 ARG cc_start: 0.6106 (mtm180) cc_final: 0.5080 (tmm160) REVERT: E 203 LYS cc_start: 0.3324 (mmtt) cc_final: 0.2220 (tptm) REVERT: E 223 SER cc_start: 0.8480 (m) cc_final: 0.8079 (t) REVERT: E 327 VAL cc_start: 0.8631 (m) cc_final: 0.8355 (p) REVERT: E 330 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8320 (ttmt) REVERT: E 345 TYR cc_start: 0.7839 (t80) cc_final: 0.7602 (t80) REVERT: F 105 MET cc_start: 0.7422 (mmp) cc_final: 0.6234 (tpp) REVERT: F 128 MET cc_start: 0.7160 (ptp) cc_final: 0.5572 (mmp) REVERT: F 220 ASP cc_start: 0.8125 (p0) cc_final: 0.7600 (m-30) REVERT: F 315 ARG cc_start: 0.6991 (ptt90) cc_final: 0.6419 (ptt90) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.2652 time to fit residues: 126.6747 Evaluate side-chains 258 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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: 0.7980 chunk 113 optimal weight: 0.0970 chunk 171 optimal weight: 0.9980 chunk 157 optimal weight: 0.0270 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 0.0970 chunk 83 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 overall best weight: 0.2172 ------------------------------------------------------------------------------- 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 340 HIS D 319 GLN E 356 GLN F 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13682 Z= 0.132 Angle : 0.579 12.721 18467 Z= 0.280 Chirality : 0.046 0.819 2200 Planarity : 0.003 0.041 2352 Dihedral : 5.605 99.117 1908 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 0.34 % Favored : 99.59 % 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: -1.56 (0.20), residues: 1712 helix: -1.00 (0.17), residues: 856 sheet: -1.41 (0.35), residues: 214 loop : -0.61 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 198 HIS 0.004 0.001 HIS A 152 PHE 0.009 0.001 PHE A 223 TYR 0.012 0.001 TYR E 357 ARG 0.006 0.000 ARG B 273 ********************** 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 330 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 329 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 CYS cc_start: 0.8825 (m) cc_final: 0.8539 (m) REVERT: A 187 ARG cc_start: 0.6888 (ptm160) cc_final: 0.6500 (ptm-80) REVERT: A 253 GLU cc_start: 0.5903 (mt-10) cc_final: 0.4742 (tm-30) REVERT: B 121 LYS cc_start: 0.7952 (ptmt) cc_final: 0.7499 (mttm) REVERT: B 127 MET cc_start: 0.8732 (mmp) cc_final: 0.8161 (mmt) REVERT: B 267 ASP cc_start: 0.8705 (m-30) cc_final: 0.8396 (t0) REVERT: B 334 ASP cc_start: 0.7228 (m-30) cc_final: 0.6931 (p0) REVERT: C 58 ASN cc_start: 0.8699 (t0) cc_final: 0.8394 (t0) REVERT: C 131 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.8253 (mtt-85) REVERT: C 132 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7439 (ttm170) REVERT: C 192 LYS cc_start: 0.7127 (ttmt) cc_final: 0.6739 (tmtt) REVERT: C 217 MET cc_start: 0.8013 (mmm) cc_final: 0.7769 (mtp) REVERT: C 225 TYR cc_start: 0.8852 (t80) cc_final: 0.8511 (t80) REVERT: D 288 ILE cc_start: 0.8222 (tp) cc_final: 0.7939 (tp) REVERT: D 297 MET cc_start: 0.6768 (tmm) cc_final: 0.6550 (tmm) REVERT: D 308 ILE cc_start: 0.8663 (mm) cc_final: 0.8268 (mm) REVERT: E 128 MET cc_start: 0.3992 (ptp) cc_final: 0.3364 (pmm) REVERT: E 199 ARG cc_start: 0.5949 (mtm180) cc_final: 0.5147 (tmm160) REVERT: E 203 LYS cc_start: 0.3077 (mmtt) cc_final: 0.2017 (tptm) REVERT: E 223 SER cc_start: 0.8536 (m) cc_final: 0.8138 (t) REVERT: E 327 VAL cc_start: 0.8599 (m) cc_final: 0.8253 (p) REVERT: E 330 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8358 (ttpt) REVERT: E 345 TYR cc_start: 0.7728 (t80) cc_final: 0.7477 (t80) REVERT: E 356 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7224 (pp30) REVERT: F 105 MET cc_start: 0.7403 (mmp) cc_final: 0.6214 (tpp) REVERT: F 128 MET cc_start: 0.6932 (ptp) cc_final: 0.5363 (mmt) REVERT: F 158 SER cc_start: 0.7893 (m) cc_final: 0.7609 (t) REVERT: F 220 ASP cc_start: 0.7981 (p0) cc_final: 0.7475 (m-30) REVERT: F 244 ASN cc_start: 0.7687 (p0) cc_final: 0.7215 (t0) outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.2472 time to fit residues: 120.4598 Evaluate side-chains 267 residues out of total 1471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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: 1.9990 chunk 125 optimal weight: 0.0070 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.0000 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5404 ------------------------------------------------------------------------------- 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** A 304 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS D 217 HIS D 319 GLN F 160 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102475 restraints weight = 27720.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104929 restraints weight = 16759.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106662 restraints weight = 11290.777| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4304 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= 0.148 Angle : 0.573 10.499 18467 Z= 0.278 Chirality : 0.045 0.618 2200 Planarity : 0.003 0.040 2352 Dihedral : 5.547 98.343 1908 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.07 % Allowed : 0.34 % Favored : 99.59 % 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: -1.41 (0.20), residues: 1712 helix: -0.89 (0.18), residues: 857 sheet: -1.27 (0.36), residues: 209 loop : -0.57 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 198 HIS 0.004 0.001 HIS A 152 PHE 0.011 0.001 PHE F 348 TYR 0.013 0.001 TYR E 357 ARG 0.006 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3234.72 seconds wall clock time: 59 minutes 41.19 seconds (3581.19 seconds total)