Starting phenix.real_space_refine on Fri Jan 19 13:14:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdw_20318/01_2024/6pdw_20318_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdw_20318/01_2024/6pdw_20318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdw_20318/01_2024/6pdw_20318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdw_20318/01_2024/6pdw_20318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdw_20318/01_2024/6pdw_20318_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdw_20318/01_2024/6pdw_20318_neut_trim_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.076 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: 8 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 50 5.16 5 Be 3 3.05 5 C 7195 2.51 5 N 2050 2.21 5 O 2164 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 303": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "D ARG 303": "NH1" <-> "NH2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 341": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 274": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E ARG 303": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 337": "NH1" <-> "NH2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 291": "NH1" <-> "NH2" Residue "F ARG 292": "NH1" <-> "NH2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 337": "NH1" <-> "NH2" Residue "F ARG 341": "NH1" <-> "NH2" Residue "F ARG 362": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 11483 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2292 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 17, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2330 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 17, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2339 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 17, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2327 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 17, 'TRANS': 280} Chain breaks: 1 Chain: "F" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2021 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.51, per 1000 atoms: 0.57 Number of scatterers: 11483 At special positions: 0 Unit cell: (80.484, 137.67, 133.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 4 11.99 F 9 9.00 O 2164 8.00 N 2050 7.00 C 7195 6.00 Be 3 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 2.1 seconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 6 sheets defined 45.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'B' and resid 45 through 64 Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.306A pdb=" N LEU B 98 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 134 through 137 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 180 through 183 No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.656A pdb=" N ILE B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 321 through 340 Proline residue: B 335 - end of helix Processing helix chain 'C' and resid 45 through 63 removed outlier: 3.944A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.871A pdb=" N GLN C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 128 through 131 No H-bonds generated for 'chain 'C' and resid 128 through 131' Processing helix chain 'C' and resid 135 through 138 removed outlier: 3.568A pdb=" N LYS C 138 " --> pdb=" O HIS C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 180 through 183 No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 215 through 218 No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.504A pdb=" N MET C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' 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 270 through 275 removed outlier: 3.952A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.931A pdb=" N ARG C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 321 through 345 removed outlier: 4.034A pdb=" N ALA C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Proline residue: C 335 - end of helix removed outlier: 4.831A pdb=" N ALA C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 63 Processing helix chain 'D' and resid 93 through 99 removed outlier: 4.255A pdb=" N LEU D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 128 through 131 No H-bonds generated for 'chain 'D' and resid 128 through 131' Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 180 through 183 No H-bonds generated for 'chain 'D' and resid 180 through 183' Processing helix chain 'D' and resid 190 through 204 removed outlier: 3.828A pdb=" N PHE D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 270 through 273 No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.544A pdb=" N ARG D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 343 Proline residue: D 335 - end of helix Processing helix chain 'E' and resid 45 through 63 Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.677A pdb=" N LEU E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.565A pdb=" N LYS E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 161 through 169 Processing helix chain 'E' and resid 180 through 183 No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 191 through 204 removed outlier: 3.708A pdb=" N LYS E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 218 No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 232 through 241 removed outlier: 3.589A pdb=" N GLU E 236 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 321 through 341 Proline residue: E 335 - end of helix Processing helix chain 'F' and resid 91 through 98 removed outlier: 3.629A pdb=" N LEU F 98 " --> pdb=" O ASN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 131 removed outlier: 4.838A pdb=" N TYR F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Proline residue: F 130 - end of helix Processing helix chain 'F' and resid 134 through 137 Processing helix chain 'F' and resid 163 through 170 Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 230 through 242 removed outlier: 3.526A pdb=" N ASP F 242 " --> pdb=" O MET F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 273 No H-bonds generated for 'chain 'F' and resid 270 through 273' Processing helix chain 'F' and resid 288 through 297 Processing helix chain 'F' and resid 309 through 316 removed outlier: 4.336A pdb=" N VAL F 315 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR F 316 " --> pdb=" O ILE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 345 removed outlier: 4.420A pdb=" N MET F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Proline residue: F 335 - end of helix removed outlier: 3.605A pdb=" N GLU F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 150 through 154 removed outlier: 6.597A pdb=" N LYS B 278 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR B 153 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE B 280 " --> pdb=" O TYR B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 175 through 178 removed outlier: 6.219A pdb=" N ILE B 209 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU B 178 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE B 211 " --> pdb=" O LEU B 178 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 278 through 281 removed outlier: 3.880A pdb=" N LYS C 278 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL C 150 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL C 258 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU C 152 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY C 260 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER C 208 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU C 259 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 210 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA C 261 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 212 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP C 213 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 278 through 281 removed outlier: 7.971A pdb=" N VAL D 150 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 258 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU D 152 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY D 260 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER D 208 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 259 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE D 210 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ALA D 261 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 212 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP D 213 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 278 through 281 removed outlier: 3.711A pdb=" N LYS E 278 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL E 150 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL E 258 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU E 152 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY E 260 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER E 208 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU E 259 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE E 210 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA E 261 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE E 212 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP E 213 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 278 through 280 removed outlier: 6.221A pdb=" N SER F 208 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU F 259 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE F 210 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA F 261 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE F 212 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE F 211 " --> pdb=" O ILE F 176 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1065 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: 3.09 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1952 1.31 - 1.44: 2775 1.44 - 1.56: 6845 1.56 - 1.69: 12 1.69 - 1.81: 91 Bond restraints: 11675 Sorted by residual: bond pdb=" N PRO B 349 " pdb=" CD PRO B 349 " ideal model delta sigma weight residual 1.473 1.690 -0.217 1.40e-02 5.10e+03 2.40e+02 bond pdb=" BE BEF B 502 " pdb=" F2 BEF B 502 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" BE BEF C 503 " pdb=" F2 BEF C 503 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" BE BEF D 502 " pdb=" F2 BEF D 502 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C ALA D 271 " pdb=" O ALA D 271 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.28e-02 6.10e+03 1.32e+01 ... (remaining 11670 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.89: 474 106.89 - 114.80: 7005 114.80 - 122.72: 7309 122.72 - 130.64: 963 130.64 - 138.56: 50 Bond angle restraints: 15801 Sorted by residual: angle pdb=" N PRO B 349 " pdb=" CA PRO B 349 " pdb=" CB PRO B 349 " ideal model delta sigma weight residual 103.36 112.01 -8.65 8.80e-01 1.29e+00 9.67e+01 angle pdb=" CA PRO B 349 " pdb=" N PRO B 349 " pdb=" CD PRO B 349 " ideal model delta sigma weight residual 112.00 100.96 11.04 1.40e+00 5.10e-01 6.22e+01 angle pdb=" C ILE D 268 " pdb=" N ASP D 269 " pdb=" CA ASP D 269 " ideal model delta sigma weight residual 121.54 133.45 -11.91 1.91e+00 2.74e-01 3.89e+01 angle pdb=" N LYS F 204 " pdb=" CA LYS F 204 " pdb=" C LYS F 204 " ideal model delta sigma weight residual 111.07 105.02 6.05 1.07e+00 8.73e-01 3.19e+01 angle pdb=" O ILE D 268 " pdb=" C ILE D 268 " pdb=" N ASP D 269 " ideal model delta sigma weight residual 121.83 127.54 -5.71 1.03e+00 9.43e-01 3.08e+01 ... (remaining 15796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.55: 7084 31.55 - 63.11: 81 63.11 - 94.66: 5 94.66 - 126.22: 2 126.22 - 157.77: 1 Dihedral angle restraints: 7173 sinusoidal: 2996 harmonic: 4177 Sorted by residual: dihedral pdb=" CA ARG D 303 " pdb=" C ARG D 303 " pdb=" N ASP D 304 " pdb=" CA ASP D 304 " ideal model delta harmonic sigma weight residual 180.00 143.35 36.65 0 5.00e+00 4.00e-02 5.37e+01 dihedral pdb=" CA ASP F 304 " pdb=" C ASP F 304 " pdb=" N PRO F 305 " pdb=" CA PRO F 305 " ideal model delta harmonic sigma weight residual 180.00 144.82 35.18 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 97.77 -157.77 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 7170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1632 0.081 - 0.162: 148 0.162 - 0.243: 4 0.243 - 0.324: 2 0.324 - 0.405: 1 Chirality restraints: 1787 Sorted by residual: chirality pdb=" CA ASP D 269 " pdb=" N ASP D 269 " pdb=" C ASP D 269 " pdb=" CB ASP D 269 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA GLU D 270 " pdb=" N GLU D 270 " pdb=" C GLU D 270 " pdb=" CB GLU D 270 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ILE D 268 " pdb=" N ILE D 268 " pdb=" C ILE D 268 " pdb=" CB ILE D 268 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1784 not shown) Planarity restraints: 2048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 267 " 0.027 2.00e-02 2.50e+03 5.53e-02 3.06e+01 pdb=" C ASP D 267 " -0.096 2.00e-02 2.50e+03 pdb=" O ASP D 267 " 0.036 2.00e-02 2.50e+03 pdb=" N ILE D 268 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 304 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO F 305 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO F 305 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 305 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 241 " 0.023 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP C 241 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP C 241 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 241 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 241 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 241 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 241 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 241 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 241 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 241 " 0.006 2.00e-02 2.50e+03 ... (remaining 2045 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 74 2.41 - 3.04: 7534 3.04 - 3.66: 17861 3.66 - 4.28: 26273 4.28 - 4.90: 42785 Nonbonded interactions: 94527 Sorted by model distance: nonbonded pdb=" O LEU D 219 " pdb=" O ILE D 268 " model vdw 1.792 3.040 nonbonded pdb=" O ALA F 202 " pdb=" O LEU F 205 " model vdw 1.961 3.040 nonbonded pdb=" OG1 THR B 161 " pdb="MG MG B 503 " model vdw 1.982 2.170 nonbonded pdb=" OG1 THR C 161 " pdb="MG MG C 502 " model vdw 1.984 2.170 nonbonded pdb=" O3B ADP E 501 " pdb="MG MG E 502 " model vdw 1.989 2.170 ... (remaining 94522 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 'B' and (resid 87 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 220 or resid 228 through 244 or \ resid 254 through 361)) selection = (chain 'C' and (resid 87 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 220 or resid 228 through 244 or \ resid 254 through 361)) selection = (chain 'D' and (resid 87 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 220 or resid 228 through 244 or \ resid 254 through 361)) selection = (chain 'E' and (resid 87 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 220 or resid 228 through 244 or \ resid 254 through 361)) selection = (chain 'F' and resid 87 through 361) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 3.720 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.700 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.050 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: 42.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 11675 Z= 0.333 Angle : 0.809 13.857 15801 Z= 0.445 Chirality : 0.047 0.405 1787 Planarity : 0.006 0.101 2048 Dihedral : 10.944 157.770 4479 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 39.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.66 % Favored : 89.27 % Rotamer: Outliers : 0.74 % Allowed : 5.67 % Favored : 93.60 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.15 % 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: -3.33 (0.20), residues: 1426 helix: -1.63 (0.17), residues: 665 sheet: -2.75 (0.34), residues: 147 loop : -2.63 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP C 241 HIS 0.010 0.001 HIS F 343 PHE 0.019 0.002 PHE B 110 TYR 0.017 0.001 TYR B 339 ARG 0.007 0.001 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 368 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 TYR cc_start: 0.8199 (m-80) cc_final: 0.7945 (m-80) REVERT: C 153 TYR cc_start: 0.8785 (p90) cc_final: 0.8526 (p90) REVERT: C 267 ASP cc_start: 0.7007 (t70) cc_final: 0.6759 (t0) REVERT: C 293 ILE cc_start: 0.8514 (mm) cc_final: 0.8295 (mt) REVERT: C 339 TYR cc_start: 0.7959 (t80) cc_final: 0.7729 (t80) REVERT: D 60 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8008 (mp) REVERT: D 111 ASN cc_start: 0.8308 (t0) cc_final: 0.8051 (t0) REVERT: D 176 ILE cc_start: 0.8423 (pt) cc_final: 0.8165 (mt) REVERT: D 269 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8401 (p0) REVERT: D 311 TYR cc_start: 0.8612 (t80) cc_final: 0.8382 (t80) REVERT: F 98 LEU cc_start: 0.9140 (mt) cc_final: 0.8865 (tt) REVERT: F 200 SER cc_start: 0.8987 (t) cc_final: 0.8592 (p) REVERT: F 269 ASP cc_start: 0.7999 (t70) cc_final: 0.7724 (t0) REVERT: F 274 ARG cc_start: 0.7141 (tmt170) cc_final: 0.6617 (ttp-170) REVERT: F 294 LEU cc_start: 0.9055 (mp) cc_final: 0.8854 (mm) outliers start: 9 outliers final: 2 residues processed: 375 average time/residue: 0.3125 time to fit residues: 152.9788 Evaluate side-chains 197 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 203 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS B 192 ASN B 248 ASN B 279 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS E 54 GLN E 192 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN F 192 ASN F 254 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11675 Z= 0.255 Angle : 0.744 8.728 15801 Z= 0.353 Chirality : 0.047 0.223 1787 Planarity : 0.006 0.096 2048 Dihedral : 8.346 169.833 1649 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.05 % Favored : 90.88 % Rotamer: Outliers : 2.71 % Allowed : 11.82 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.22), residues: 1426 helix: -0.66 (0.20), residues: 676 sheet: -2.06 (0.38), residues: 147 loop : -2.12 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 241 HIS 0.005 0.001 HIS F 169 PHE 0.019 0.002 PHE B 110 TYR 0.011 0.001 TYR E 153 ARG 0.009 0.001 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.8866 (tpt) cc_final: 0.8621 (tpt) REVERT: C 153 TYR cc_start: 0.8763 (p90) cc_final: 0.8525 (p90) REVERT: C 267 ASP cc_start: 0.6946 (t70) cc_final: 0.6720 (t0) REVERT: C 293 ILE cc_start: 0.8530 (mm) cc_final: 0.8267 (mt) REVERT: D 111 ASN cc_start: 0.8294 (t0) cc_final: 0.8034 (t0) REVERT: D 269 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7944 (p0) REVERT: E 51 ILE cc_start: 0.8213 (tt) cc_final: 0.7918 (tt) REVERT: E 196 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.7324 (ttp-170) REVERT: E 232 MET cc_start: 0.8828 (ttm) cc_final: 0.8508 (ttp) REVERT: E 336 MET cc_start: 0.8387 (tpp) cc_final: 0.8146 (mmt) REVERT: F 144 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8377 (pp) REVERT: F 269 ASP cc_start: 0.8114 (t70) cc_final: 0.7876 (t0) REVERT: F 319 MET cc_start: 0.7601 (mtp) cc_final: 0.6978 (mtp) outliers start: 33 outliers final: 13 residues processed: 235 average time/residue: 0.2663 time to fit residues: 85.6119 Evaluate side-chains 198 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 254 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11675 Z= 0.274 Angle : 0.737 9.108 15801 Z= 0.349 Chirality : 0.046 0.219 1787 Planarity : 0.006 0.081 2048 Dihedral : 8.168 175.254 1641 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.47 % Favored : 90.46 % Rotamer: Outliers : 3.94 % Allowed : 13.14 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.22 % 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 (0.22), residues: 1426 helix: -0.37 (0.20), residues: 689 sheet: -1.92 (0.39), residues: 152 loop : -1.96 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 241 HIS 0.022 0.001 HIS C 343 PHE 0.017 0.002 PHE D 175 TYR 0.016 0.001 TYR F 339 ARG 0.008 0.001 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 GLN cc_start: 0.8289 (mt0) cc_final: 0.8032 (mt0) REVERT: B 336 MET cc_start: 0.8836 (tpt) cc_final: 0.8571 (tpt) REVERT: C 151 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8857 (tm) REVERT: C 153 TYR cc_start: 0.8843 (p90) cc_final: 0.8629 (p90) REVERT: C 176 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8024 (mt) REVERT: C 267 ASP cc_start: 0.6948 (t70) cc_final: 0.6643 (t0) REVERT: C 293 ILE cc_start: 0.8546 (mm) cc_final: 0.8342 (mt) REVERT: C 342 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 343 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.7606 (t-90) REVERT: C 353 ILE cc_start: 0.8125 (pp) cc_final: 0.7861 (tp) REVERT: D 111 ASN cc_start: 0.8415 (t0) cc_final: 0.8177 (t0) REVERT: E 51 ILE cc_start: 0.8327 (tt) cc_final: 0.8016 (tt) REVERT: E 232 MET cc_start: 0.8829 (ttm) cc_final: 0.8548 (ttp) REVERT: E 336 MET cc_start: 0.8399 (tpp) cc_final: 0.8165 (mmt) REVERT: F 94 ASN cc_start: 0.8675 (m-40) cc_final: 0.8239 (m110) REVERT: F 289 GLN cc_start: 0.9116 (pm20) cc_final: 0.8758 (pm20) outliers start: 48 outliers final: 26 residues processed: 231 average time/residue: 0.2435 time to fit residues: 79.4048 Evaluate side-chains 201 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 304 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 HIS C 343 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11675 Z= 0.198 Angle : 0.714 10.979 15801 Z= 0.331 Chirality : 0.045 0.214 1787 Planarity : 0.005 0.076 2048 Dihedral : 7.878 168.598 1641 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.79 % Allowed : 14.94 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.22 % 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: -1.46 (0.23), residues: 1426 helix: -0.09 (0.20), residues: 697 sheet: -1.58 (0.41), residues: 151 loop : -1.81 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 241 HIS 0.007 0.001 HIS C 343 PHE 0.014 0.002 PHE C 175 TYR 0.013 0.001 TYR F 339 ARG 0.005 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: B 58 ARG cc_start: 0.7074 (ttm170) cc_final: 0.6817 (ttm110) REVERT: B 59 ARG cc_start: 0.7429 (mmm160) cc_final: 0.6962 (tmt170) REVERT: B 133 MET cc_start: 0.8759 (ppp) cc_final: 0.8444 (ppp) REVERT: B 254 ASN cc_start: 0.7292 (m110) cc_final: 0.7049 (m110) REVERT: B 336 MET cc_start: 0.8817 (tpt) cc_final: 0.8530 (tpt) REVERT: C 151 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8822 (tp) REVERT: C 153 TYR cc_start: 0.8789 (p90) cc_final: 0.8583 (p90) REVERT: C 267 ASP cc_start: 0.6792 (t70) cc_final: 0.6552 (t0) REVERT: C 293 ILE cc_start: 0.8552 (mm) cc_final: 0.8350 (mt) REVERT: C 342 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8276 (tm-30) REVERT: C 353 ILE cc_start: 0.8269 (pp) cc_final: 0.8029 (tp) REVERT: E 51 ILE cc_start: 0.8299 (tt) cc_final: 0.7966 (tt) REVERT: E 104 GLU cc_start: 0.8109 (tp30) cc_final: 0.7863 (tp30) REVERT: E 232 MET cc_start: 0.8795 (ttm) cc_final: 0.8481 (ttp) REVERT: F 94 ASN cc_start: 0.8670 (m-40) cc_final: 0.8369 (m-40) REVERT: F 325 LYS cc_start: 0.3101 (mttt) cc_final: 0.2787 (mttm) outliers start: 34 outliers final: 22 residues processed: 217 average time/residue: 0.2344 time to fit residues: 71.7931 Evaluate side-chains 191 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 20.0000 chunk 78 optimal weight: 0.0980 chunk 2 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN D 343 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11675 Z= 0.239 Angle : 0.709 9.107 15801 Z= 0.331 Chirality : 0.045 0.227 1787 Planarity : 0.005 0.070 2048 Dihedral : 7.771 164.003 1641 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.12 % Allowed : 15.35 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.29 (0.23), residues: 1426 helix: 0.02 (0.20), residues: 699 sheet: -1.45 (0.41), residues: 151 loop : -1.71 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 241 HIS 0.004 0.001 HIS F 343 PHE 0.016 0.002 PHE C 175 TYR 0.011 0.001 TYR B 188 ARG 0.006 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7378 (mmm160) cc_final: 0.6958 (tmt170) REVERT: B 133 MET cc_start: 0.8749 (ppp) cc_final: 0.8388 (ppp) REVERT: B 336 MET cc_start: 0.8820 (tpt) cc_final: 0.8505 (tpt) REVERT: C 151 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8835 (tm) REVERT: C 176 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.7948 (mt) REVERT: C 342 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 353 ILE cc_start: 0.8273 (pp) cc_final: 0.8018 (tp) REVERT: D 268 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8481 (mm) REVERT: E 51 ILE cc_start: 0.8355 (tt) cc_final: 0.8007 (tt) REVERT: E 104 GLU cc_start: 0.8087 (tp30) cc_final: 0.7861 (tp30) REVERT: E 138 LYS cc_start: 0.8563 (tppt) cc_final: 0.8201 (tptt) REVERT: E 242 ASP cc_start: 0.8476 (t0) cc_final: 0.8256 (t0) REVERT: F 137 TYR cc_start: 0.7813 (m-80) cc_final: 0.7501 (m-80) REVERT: F 325 LYS cc_start: 0.2987 (mttt) cc_final: 0.2573 (mttm) outliers start: 38 outliers final: 25 residues processed: 202 average time/residue: 0.2535 time to fit residues: 71.5308 Evaluate side-chains 192 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 HIS E 192 ASN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11675 Z= 0.222 Angle : 0.700 8.506 15801 Z= 0.327 Chirality : 0.044 0.230 1787 Planarity : 0.005 0.070 2048 Dihedral : 7.683 162.889 1641 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 3.12 % Allowed : 15.68 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.18 (0.23), residues: 1426 helix: 0.15 (0.20), residues: 696 sheet: -1.33 (0.42), residues: 151 loop : -1.74 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 241 HIS 0.005 0.001 HIS F 343 PHE 0.019 0.002 PHE F 307 TYR 0.016 0.001 TYR B 137 ARG 0.004 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.8902 (mp) cc_final: 0.8695 (mp) REVERT: C 151 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8830 (tm) REVERT: C 176 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7937 (mt) REVERT: C 342 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 353 ILE cc_start: 0.8366 (pp) cc_final: 0.8112 (tp) REVERT: D 268 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8514 (mm) REVERT: E 51 ILE cc_start: 0.8350 (tt) cc_final: 0.7987 (tt) REVERT: E 104 GLU cc_start: 0.8095 (tp30) cc_final: 0.7889 (tp30) REVERT: E 138 LYS cc_start: 0.8536 (tppt) cc_final: 0.8207 (tptt) REVERT: E 242 ASP cc_start: 0.8554 (t0) cc_final: 0.8240 (t0) REVERT: F 304 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6953 (m-30) outliers start: 38 outliers final: 27 residues processed: 199 average time/residue: 0.2829 time to fit residues: 78.5574 Evaluate side-chains 190 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11675 Z= 0.214 Angle : 0.701 10.925 15801 Z= 0.327 Chirality : 0.044 0.228 1787 Planarity : 0.005 0.066 2048 Dihedral : 7.584 160.355 1641 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.12 % Allowed : 16.42 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1426 helix: 0.28 (0.20), residues: 692 sheet: -1.26 (0.42), residues: 151 loop : -1.74 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 241 HIS 0.004 0.001 HIS F 343 PHE 0.020 0.002 PHE F 307 TYR 0.018 0.001 TYR D 311 ARG 0.003 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 170 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.8898 (mp) cc_final: 0.8682 (mp) REVERT: C 151 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8799 (tm) REVERT: C 176 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.7923 (mt) REVERT: C 342 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8373 (tm-30) REVERT: C 353 ILE cc_start: 0.8375 (pp) cc_final: 0.8081 (tp) REVERT: D 268 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8480 (mm) REVERT: E 51 ILE cc_start: 0.8353 (tt) cc_final: 0.7993 (tt) REVERT: E 59 ARG cc_start: 0.6334 (tpp80) cc_final: 0.5493 (mpp80) REVERT: E 138 LYS cc_start: 0.8547 (tppt) cc_final: 0.8237 (tptt) REVERT: E 242 ASP cc_start: 0.8556 (t0) cc_final: 0.8229 (t0) REVERT: F 94 ASN cc_start: 0.8404 (m-40) cc_final: 0.8114 (m110) REVERT: F 304 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6861 (m-30) outliers start: 38 outliers final: 28 residues processed: 200 average time/residue: 0.2734 time to fit residues: 77.7575 Evaluate side-chains 193 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 125 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11675 Z= 0.208 Angle : 0.700 9.794 15801 Z= 0.328 Chirality : 0.044 0.230 1787 Planarity : 0.005 0.065 2048 Dihedral : 7.494 157.718 1641 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.96 % Allowed : 16.91 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1426 helix: 0.37 (0.21), residues: 691 sheet: -1.16 (0.42), residues: 152 loop : -1.72 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 241 HIS 0.005 0.001 HIS F 343 PHE 0.021 0.002 PHE F 307 TYR 0.016 0.001 TYR B 137 ARG 0.004 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 172 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.8915 (mp) cc_final: 0.8696 (mp) REVERT: C 58 ARG cc_start: 0.6414 (ttm170) cc_final: 0.6124 (ttm170) REVERT: C 151 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8787 (tm) REVERT: C 176 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 353 ILE cc_start: 0.8335 (pp) cc_final: 0.8009 (tp) REVERT: D 268 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8489 (mm) REVERT: E 51 ILE cc_start: 0.8383 (tt) cc_final: 0.8030 (tt) REVERT: E 59 ARG cc_start: 0.6322 (tpp80) cc_final: 0.5548 (mpp80) REVERT: E 138 LYS cc_start: 0.8540 (tppt) cc_final: 0.8243 (tptt) REVERT: E 242 ASP cc_start: 0.8586 (t0) cc_final: 0.8234 (t0) REVERT: F 94 ASN cc_start: 0.8404 (m-40) cc_final: 0.8079 (m110) REVERT: F 304 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: F 325 LYS cc_start: 0.3682 (mttt) cc_final: 0.3435 (mttm) outliers start: 36 outliers final: 29 residues processed: 202 average time/residue: 0.2571 time to fit residues: 72.4010 Evaluate side-chains 197 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 39 optimal weight: 0.0470 chunk 116 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 343 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11675 Z= 0.196 Angle : 0.691 10.241 15801 Z= 0.325 Chirality : 0.044 0.232 1787 Planarity : 0.004 0.062 2048 Dihedral : 7.385 154.247 1641 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.63 % Allowed : 17.57 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1426 helix: 0.43 (0.21), residues: 694 sheet: -1.04 (0.43), residues: 152 loop : -1.67 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 187 HIS 0.006 0.001 HIS F 343 PHE 0.021 0.002 PHE F 307 TYR 0.019 0.001 TYR D 311 ARG 0.004 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.8910 (mp) cc_final: 0.8689 (mp) REVERT: C 93 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 151 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8770 (tm) REVERT: C 176 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7844 (mt) REVERT: C 353 ILE cc_start: 0.8408 (pp) cc_final: 0.8098 (tp) REVERT: D 268 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8453 (mm) REVERT: E 51 ILE cc_start: 0.8384 (tt) cc_final: 0.8028 (tt) REVERT: E 59 ARG cc_start: 0.6313 (tpp80) cc_final: 0.5615 (mpp80) REVERT: E 138 LYS cc_start: 0.8539 (tppt) cc_final: 0.8247 (tptt) REVERT: E 242 ASP cc_start: 0.8568 (t0) cc_final: 0.8252 (t0) REVERT: E 361 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6648 (pp) REVERT: F 94 ASN cc_start: 0.8410 (m-40) cc_final: 0.8098 (m110) REVERT: F 304 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6753 (m-30) outliers start: 32 outliers final: 27 residues processed: 203 average time/residue: 0.2585 time to fit residues: 72.6127 Evaluate side-chains 198 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 chunk 94 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11675 Z= 0.214 Angle : 0.704 10.791 15801 Z= 0.333 Chirality : 0.044 0.235 1787 Planarity : 0.005 0.062 2048 Dihedral : 7.347 150.420 1641 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.79 % Allowed : 17.57 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1426 helix: 0.46 (0.21), residues: 687 sheet: -0.94 (0.43), residues: 152 loop : -1.68 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 187 HIS 0.006 0.001 HIS F 343 PHE 0.023 0.002 PHE F 307 TYR 0.014 0.001 TYR B 137 ARG 0.015 0.000 ARG E 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 MET cc_start: 0.8555 (ppp) cc_final: 0.8245 (ppp) REVERT: C 93 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 151 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8777 (tm) REVERT: C 176 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7880 (mt) REVERT: C 353 ILE cc_start: 0.8410 (pp) cc_final: 0.8063 (tp) REVERT: D 223 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7560 (mtm110) REVERT: D 268 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8466 (mm) REVERT: D 311 TYR cc_start: 0.8486 (t80) cc_final: 0.8171 (t80) REVERT: D 333 MET cc_start: 0.8070 (tpp) cc_final: 0.7610 (mmm) REVERT: E 51 ILE cc_start: 0.8351 (tt) cc_final: 0.8002 (tt) REVERT: E 59 ARG cc_start: 0.6321 (tpp80) cc_final: 0.5624 (mpp80) REVERT: E 138 LYS cc_start: 0.8540 (tppt) cc_final: 0.8245 (tptt) REVERT: E 242 ASP cc_start: 0.8598 (t0) cc_final: 0.8229 (t0) REVERT: E 361 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6577 (pp) REVERT: F 94 ASN cc_start: 0.8413 (m-40) cc_final: 0.8098 (m110) REVERT: F 304 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6840 (m-30) outliers start: 34 outliers final: 28 residues processed: 202 average time/residue: 0.2612 time to fit residues: 73.7212 Evaluate side-chains 197 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107126 restraints weight = 17029.789| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.59 r_work: 0.3182 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11675 Z= 0.215 Angle : 0.705 10.181 15801 Z= 0.333 Chirality : 0.044 0.237 1787 Planarity : 0.005 0.060 2048 Dihedral : 7.300 148.094 1641 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.96 % Allowed : 17.57 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1426 helix: 0.47 (0.21), residues: 693 sheet: -0.87 (0.44), residues: 152 loop : -1.61 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 187 HIS 0.007 0.001 HIS F 169 PHE 0.022 0.002 PHE F 307 TYR 0.012 0.001 TYR B 188 ARG 0.011 0.000 ARG E 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.26 seconds wall clock time: 49 minutes 32.94 seconds (2972.94 seconds total)