Starting phenix.real_space_refine on Fri Mar 15 23:46:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdy_20319/03_2024/6pdy_20319_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdy_20319/03_2024/6pdy_20319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdy_20319/03_2024/6pdy_20319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdy_20319/03_2024/6pdy_20319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdy_20319/03_2024/6pdy_20319_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdy_20319/03_2024/6pdy_20319_neut_trim_updated.pdb" } resolution = 3.7 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= 0.006 sd= 0.058 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 10 5.49 5 Mg 4 5.21 5 S 59 5.16 5 Be 4 3.05 5 C 8216 2.51 5 N 2330 2.21 5 O 2461 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 196": "NH1" <-> "NH2" Residue "F ARG 264": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F ARG 303": "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 "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 275": "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 "B ARG 344": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 223": "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 "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" 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 196": "NH1" <-> "NH2" Residue "E ARG 274": "NH1" <-> "NH2" Residue "E ARG 275": "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" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13096 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1831 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 2 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2048 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 245} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2209 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2327 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2293 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 275} Chain breaks: 1 Chain: "E" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2183 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 1 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: "A" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.49, per 1000 atoms: 0.57 Number of scatterers: 13096 At special positions: 0 Unit cell: (85.779, 138.729, 136.611, 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 59 16.00 P 10 15.00 Mg 4 11.99 F 12 9.00 O 2461 8.00 N 2330 7.00 C 8216 6.00 Be 4 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=0, symmetry=0 Time building additional restraints: 5.08 Conformation dependent library (CDL) restraints added in 2.1 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 5 sheets defined 42.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'F' and resid 91 through 98 removed outlier: 4.287A pdb=" N LEU F 98 " --> pdb=" O ASN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 128 through 131 No H-bonds generated for 'chain 'F' and resid 128 through 131' Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.706A pdb=" N ALA F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS F 169 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 183 Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.656A pdb=" N PHE F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.795A pdb=" N MET F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 289 through 299 Processing helix chain 'F' and resid 311 through 315 removed outlier: 3.614A pdb=" N VAL F 315 " --> pdb=" O ILE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.697A pdb=" N CYS F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 91 through 94 No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 128 through 131 No H-bonds generated for 'chain 'A' and resid 128 through 131' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 193 through 204 removed outlier: 3.661A pdb=" N PHE A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 270 through 273 No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 321 through 345 Proline residue: A 335 - end of helix removed outlier: 4.137A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 64 Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.690A pdb=" N LEU B 98 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.820A pdb=" N LYS B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 134 through 137 Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 192 through 204 removed outlier: 3.612A pdb=" N PHE B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 removed outlier: 4.012A pdb=" N VAL B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 273 No H-bonds generated for 'chain 'B' and resid 270 through 273' Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.543A pdb=" N GLU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 removed outlier: 3.603A pdb=" N THR B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 341 through 344 No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'C' and resid 45 through 63 removed outlier: 3.825A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.810A pdb=" N GLN C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 118 through 124 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 134 through 137 Processing helix chain 'C' and resid 160 through 169 removed outlier: 3.524A pdb=" N LYS C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 166 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) 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 removed outlier: 3.757A pdb=" N ILE C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C 195 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 241 removed outlier: 3.517A pdb=" N LYS C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) 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 273 No H-bonds generated for 'chain 'C' and resid 270 through 273' Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 323 through 330 Processing helix chain 'C' and resid 334 through 345 removed outlier: 4.260A pdb=" N ALA C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 63 removed outlier: 3.686A pdb=" N ILE D 60 " --> pdb=" O ASN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.879A pdb=" N GLN D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 96 " --> pdb=" O TYR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 122 through 125 No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 162 through 167 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: 3.571A pdb=" N VAL D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 218 No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 237 through 240 No H-bonds generated for 'chain 'D' and resid 237 through 240' Processing helix chain 'D' and resid 272 through 275 No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 289 through 297 removed outlier: 3.512A pdb=" N GLU D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 323 through 341 removed outlier: 4.034A pdb=" N ALA D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Proline residue: D 335 - end of helix Processing helix chain 'E' and resid 45 through 63 Processing helix chain 'E' and resid 93 through 99 removed outlier: 3.859A pdb=" N LEU E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 125 removed outlier: 3.554A pdb=" N GLU E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 131 No H-bonds generated for 'chain 'E' and resid 128 through 131' Processing helix chain 'E' and resid 136 through 139 removed outlier: 4.136A pdb=" N HIS E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 162 through 169 Processing helix chain 'E' and resid 180 through 182 No H-bonds generated for 'chain 'E' and resid 180 through 182' Processing helix chain 'E' and resid 192 through 204 removed outlier: 3.667A pdb=" N PHE E 199 " --> pdb=" O VAL E 195 " (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 228 through 241 removed outlier: 3.620A pdb=" N VAL E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA E 235 " --> pdb=" O GLY E 231 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 236 " --> pdb=" O MET E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'E' and resid 321 through 341 removed outlier: 3.903A pdb=" N LYS E 325 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 329 " --> pdb=" O LYS E 325 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ALA E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Proline residue: E 335 - end of helix removed outlier: 4.342A pdb=" N GLU E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR E 339 " --> pdb=" O PRO E 335 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE E 340 " --> pdb=" O MET E 336 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 341 " --> pdb=" O ARG E 337 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'F' and resid 278 through 281 removed outlier: 6.508A pdb=" N VAL F 258 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU F 152 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY F 260 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE F 210 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA F 261 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 212 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 150 through 154 removed outlier: 6.364A pdb=" N LYS C 278 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR C 153 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE C 280 " --> pdb=" O TYR C 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.755A pdb=" N VAL C 257 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 278 through 282 removed outlier: 3.814A pdb=" N LYS D 278 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL D 150 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL D 258 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU D 152 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY D 260 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N GLY D 154 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR D 262 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER D 208 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU D 259 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 210 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA D 261 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE D 212 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER D 174 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE D 211 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE D 176 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASP D 213 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 278 through 282 removed outlier: 3.969A pdb=" N LYS E 278 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL E 258 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU E 152 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY E 260 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY E 154 " --> pdb=" O GLY E 260 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 261 " --> pdb=" O ILE E 212 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 966 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: 3.02 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3422 1.33 - 1.45: 2082 1.45 - 1.57: 7689 1.57 - 1.69: 15 1.69 - 1.81: 106 Bond restraints: 13314 Sorted by residual: bond pdb=" BE BEF A 502 " pdb=" F2 BEF A 502 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" BE BEF C 502 " pdb=" F2 BEF C 502 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 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 1.83e+01 bond pdb=" BE BEF E 501 " pdb=" F2 BEF E 501 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" BE BEF E 501 " pdb=" F3 BEF E 501 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 13309 not shown) Histogram of bond angle deviations from ideal: 99.73 - 107.01: 534 107.01 - 114.29: 7859 114.29 - 121.57: 6587 121.57 - 128.85: 2965 128.85 - 136.13: 73 Bond angle restraints: 18018 Sorted by residual: angle pdb=" C ILE B 340 " pdb=" N ARG B 341 " pdb=" CA ARG B 341 " ideal model delta sigma weight residual 120.28 126.72 -6.44 1.44e+00 4.82e-01 2.00e+01 angle pdb=" C ILE C 215 " pdb=" CA ILE C 215 " pdb=" CB ILE C 215 " ideal model delta sigma weight residual 111.29 104.19 7.10 1.64e+00 3.72e-01 1.87e+01 angle pdb=" F2 BEF B 502 " pdb=" BE BEF B 502 " pdb=" F3 BEF B 502 " ideal model delta sigma weight residual 119.96 107.17 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" F2 BEF E 501 " pdb=" BE BEF E 501 " pdb=" F3 BEF E 501 " ideal model delta sigma weight residual 119.96 107.23 12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" F2 BEF C 502 " pdb=" BE BEF C 502 " pdb=" F3 BEF C 502 " ideal model delta sigma weight residual 119.96 107.28 12.68 3.00e+00 1.11e-01 1.79e+01 ... (remaining 18013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 8128 35.89 - 71.77: 41 71.77 - 107.66: 4 107.66 - 143.54: 4 143.54 - 179.43: 1 Dihedral angle restraints: 8178 sinusoidal: 3421 harmonic: 4757 Sorted by residual: dihedral pdb=" CA GLN B 206 " pdb=" C GLN B 206 " pdb=" N PRO B 207 " pdb=" CA PRO B 207 " ideal model delta harmonic sigma weight residual 180.00 137.20 42.80 0 5.00e+00 4.00e-02 7.33e+01 dihedral pdb=" CA TYR B 129 " pdb=" C TYR B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 140.75 39.25 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" CA TYR D 129 " pdb=" C TYR D 129 " pdb=" N PRO D 130 " pdb=" CA PRO D 130 " ideal model delta harmonic sigma weight residual 180.00 141.41 38.59 0 5.00e+00 4.00e-02 5.96e+01 ... (remaining 8175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1782 0.065 - 0.129: 240 0.129 - 0.194: 17 0.194 - 0.259: 0 0.259 - 0.323: 3 Chirality restraints: 2042 Sorted by residual: chirality pdb=" CA HIS B 343 " pdb=" N HIS B 343 " pdb=" C HIS B 343 " pdb=" CB HIS B 343 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA GLU C 214 " pdb=" N GLU C 214 " pdb=" C GLU C 214 " pdb=" CB GLU C 214 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE C 212 " pdb=" N ILE C 212 " pdb=" C ILE C 212 " pdb=" CB ILE C 212 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2039 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 129 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO B 130 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 129 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO D 130 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 106 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO F 107 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 107 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 107 " -0.035 5.00e-02 4.00e+02 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 14 2.11 - 2.81: 3837 2.81 - 3.51: 19934 3.51 - 4.20: 30874 4.20 - 4.90: 51807 Nonbonded interactions: 106466 Sorted by model distance: nonbonded pdb=" OD2 ASP C 213 " pdb="MG MG C 503 " model vdw 1.416 2.170 nonbonded pdb=" BE BEF B 502 " pdb="MG MG B 503 " model vdw 1.762 1.550 nonbonded pdb=" OD2 ASP D 213 " pdb="MG MG D 502 " model vdw 2.017 2.170 nonbonded pdb=" OG1 THR B 161 " pdb="MG MG B 503 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASP D 213 " pdb="MG MG D 502 " model vdw 2.051 2.170 ... (remaining 106461 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 48 through 64 or resid 87 through 342)) selection = (chain 'B' and (resid 48 through 64 or resid 87 through 132 or resid 145 through \ 220 or (resid 228 through 229 and (name N or name CA or name C or name O or nam \ e CB )) or resid 230 through 243 or resid 252 through 342)) selection = (chain 'C' and (resid 48 through 64 or resid 87 through 132 or resid 145 through \ 220 or (resid 228 through 229 and (name N or name CA or name C or name O or nam \ e CB )) or resid 230 through 243 or resid 252 through 342)) selection = (chain 'D' and (resid 48 through 132 or resid 145 through 220 or (resid 228 thro \ ugh 229 and (name N or name CA or name C or name O or name CB )) or resid 230 th \ rough 243 or resid 252 through 342)) selection = (chain 'E' and (resid 48 through 64 or resid 87 through 132 or resid 145 through \ 220 or (resid 228 through 229 and (name N or name CA or name C or name O or nam \ e CB )) or resid 230 through 243 or resid 252 through 342)) } 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 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: 1.150 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: 3.930 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.810 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.004 0.086 13314 Z= 0.242 Angle : 0.799 12.789 18018 Z= 0.448 Chirality : 0.045 0.323 2042 Planarity : 0.006 0.108 2325 Dihedral : 11.278 179.426 5106 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 47.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.82 % Favored : 89.12 % Rotamer: Outliers : 0.65 % Allowed : 1.73 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -4.29 (0.18), residues: 1618 helix: -2.43 (0.15), residues: 713 sheet: -3.16 (0.37), residues: 148 loop : -3.17 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 241 HIS 0.006 0.001 HIS B 343 PHE 0.012 0.001 PHE E 307 TYR 0.016 0.001 TYR D 129 ARG 0.005 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 360 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 169 HIS cc_start: 0.8237 (t-90) cc_final: 0.7985 (t-90) REVERT: F 177 ASN cc_start: 0.8411 (t0) cc_final: 0.7953 (t0) REVERT: F 178 LEU cc_start: 0.8702 (tp) cc_final: 0.8300 (tp) REVERT: F 192 ASN cc_start: 0.8378 (t0) cc_final: 0.6519 (t0) REVERT: F 336 MET cc_start: 0.7759 (tpt) cc_final: 0.7464 (tpp) REVERT: A 94 ASN cc_start: 0.7473 (m-40) cc_final: 0.7081 (m-40) REVERT: A 201 LEU cc_start: 0.9051 (tp) cc_final: 0.8664 (pp) REVERT: B 54 GLN cc_start: 0.8921 (mt0) cc_final: 0.8261 (mm-40) REVERT: B 188 TYR cc_start: 0.7606 (t80) cc_final: 0.7406 (t80) REVERT: B 333 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8358 (mtm) REVERT: C 122 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7846 (mt-10) REVERT: D 242 ASP cc_start: 0.7615 (p0) cc_final: 0.7287 (t0) REVERT: E 237 PHE cc_start: 0.9008 (t80) cc_final: 0.8783 (t80) outliers start: 9 outliers final: 6 residues processed: 367 average time/residue: 0.3390 time to fit residues: 163.6895 Evaluate side-chains 212 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 205 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 192 ASN B 289 GLN C 94 ASN C 289 GLN D 46 ASN D 206 GLN D 248 ASN D 342 GLN E 54 GLN E 179 HIS ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13314 Z= 0.282 Angle : 0.825 11.654 18018 Z= 0.393 Chirality : 0.049 0.225 2042 Planarity : 0.007 0.100 2325 Dihedral : 9.751 160.505 1888 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.37 % Favored : 88.50 % Rotamer: Outliers : 2.52 % Allowed : 10.45 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -3.47 (0.19), residues: 1618 helix: -1.62 (0.17), residues: 723 sheet: -2.47 (0.41), residues: 141 loop : -2.96 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 241 HIS 0.012 0.001 HIS E 179 PHE 0.015 0.002 PHE C 307 TYR 0.020 0.002 TYR D 339 ARG 0.011 0.001 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8932 (m-80) cc_final: 0.8669 (m-80) REVERT: F 169 HIS cc_start: 0.8138 (t-90) cc_final: 0.7890 (t-90) REVERT: F 177 ASN cc_start: 0.8370 (t0) cc_final: 0.7965 (t0) REVERT: F 178 LEU cc_start: 0.8778 (tp) cc_final: 0.8417 (tp) REVERT: F 192 ASN cc_start: 0.7181 (t0) cc_final: 0.5666 (t0) REVERT: A 201 LEU cc_start: 0.8976 (tp) cc_final: 0.8729 (pp) REVERT: A 333 MET cc_start: 0.8727 (ttm) cc_final: 0.8372 (tmm) REVERT: B 238 MET cc_start: 0.7362 (mtt) cc_final: 0.7088 (mtt) REVERT: C 55 GLU cc_start: 0.5576 (mp0) cc_final: 0.5373 (mp0) REVERT: D 52 LYS cc_start: 0.9389 (mmmt) cc_final: 0.8839 (mmtm) REVERT: D 98 LEU cc_start: 0.8774 (pp) cc_final: 0.8531 (tp) REVERT: E 193 LYS cc_start: 0.8276 (mttp) cc_final: 0.7757 (mtmt) outliers start: 35 outliers final: 19 residues processed: 249 average time/residue: 0.2645 time to fit residues: 93.4400 Evaluate side-chains 209 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 40 optimal weight: 0.0170 chunk 148 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 ASN A 279 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 179 HIS ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13314 Z= 0.215 Angle : 0.799 12.874 18018 Z= 0.373 Chirality : 0.047 0.246 2042 Planarity : 0.006 0.096 2325 Dihedral : 9.011 145.503 1873 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 2.74 % Allowed : 12.61 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -3.04 (0.19), residues: 1618 helix: -1.22 (0.18), residues: 729 sheet: -2.21 (0.39), residues: 159 loop : -2.79 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 241 HIS 0.008 0.001 HIS F 179 PHE 0.021 0.002 PHE A 175 TYR 0.020 0.002 TYR B 129 ARG 0.008 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 213 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8937 (m-80) cc_final: 0.8609 (m-80) REVERT: F 169 HIS cc_start: 0.8113 (t-90) cc_final: 0.7868 (t-90) REVERT: F 177 ASN cc_start: 0.8309 (t0) cc_final: 0.7940 (t0) REVERT: F 178 LEU cc_start: 0.8792 (tp) cc_final: 0.8439 (tp) REVERT: F 274 ARG cc_start: 0.8052 (tmm160) cc_final: 0.7594 (tmm160) REVERT: F 276 MET cc_start: 0.9226 (tpp) cc_final: 0.9005 (tpp) REVERT: A 201 LEU cc_start: 0.8964 (tp) cc_final: 0.8729 (pp) REVERT: A 333 MET cc_start: 0.8719 (ttm) cc_final: 0.8364 (tmm) REVERT: B 238 MET cc_start: 0.7484 (mtt) cc_final: 0.7228 (mtt) REVERT: C 123 LEU cc_start: 0.9171 (tp) cc_final: 0.8967 (tt) REVERT: C 205 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8593 (pp) REVERT: C 227 HIS cc_start: 0.6550 (t-90) cc_final: 0.6267 (t-90) outliers start: 38 outliers final: 19 residues processed: 236 average time/residue: 0.2689 time to fit residues: 91.3626 Evaluate side-chains 211 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 42 optimal weight: 0.0060 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13314 Z= 0.220 Angle : 0.783 12.376 18018 Z= 0.367 Chirality : 0.047 0.200 2042 Planarity : 0.006 0.095 2325 Dihedral : 8.675 127.269 1871 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.37 % Favored : 88.57 % Rotamer: Outliers : 2.59 % Allowed : 15.42 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -2.74 (0.20), residues: 1618 helix: -0.96 (0.18), residues: 730 sheet: -1.91 (0.40), residues: 155 loop : -2.70 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 241 HIS 0.010 0.001 HIS F 179 PHE 0.024 0.002 PHE A 175 TYR 0.017 0.001 TYR A 129 ARG 0.010 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 207 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 119 ILE cc_start: 0.8297 (mm) cc_final: 0.8083 (mp) REVERT: F 169 HIS cc_start: 0.8163 (t-90) cc_final: 0.7897 (t-90) REVERT: F 177 ASN cc_start: 0.8276 (t0) cc_final: 0.7956 (t0) REVERT: F 178 LEU cc_start: 0.8785 (tp) cc_final: 0.8479 (tp) REVERT: F 239 THR cc_start: 0.8270 (m) cc_final: 0.7351 (m) REVERT: F 274 ARG cc_start: 0.8052 (tmm160) cc_final: 0.7455 (tmm160) REVERT: F 276 MET cc_start: 0.9144 (tpp) cc_final: 0.8472 (tpp) REVERT: A 175 PHE cc_start: 0.6362 (t80) cc_final: 0.6080 (t80) REVERT: A 177 ASN cc_start: 0.6123 (t0) cc_final: 0.5911 (t0) REVERT: A 179 HIS cc_start: 0.6980 (m-70) cc_final: 0.6682 (m-70) REVERT: A 333 MET cc_start: 0.8650 (ttm) cc_final: 0.8378 (tmm) REVERT: B 99 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8012 (mm-30) REVERT: E 238 MET cc_start: 0.7714 (ptt) cc_final: 0.7462 (ptt) outliers start: 36 outliers final: 22 residues processed: 229 average time/residue: 0.2535 time to fit residues: 83.8986 Evaluate side-chains 210 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.0270 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.0070 chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS B 177 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13314 Z= 0.187 Angle : 0.775 14.320 18018 Z= 0.360 Chirality : 0.046 0.197 2042 Planarity : 0.006 0.092 2325 Dihedral : 8.408 122.043 1871 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.31 % Allowed : 15.92 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -2.56 (0.20), residues: 1618 helix: -0.83 (0.19), residues: 725 sheet: -1.82 (0.41), residues: 150 loop : -2.57 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 241 HIS 0.012 0.001 HIS F 179 PHE 0.022 0.002 PHE A 175 TYR 0.019 0.001 TYR A 129 ARG 0.005 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 119 ILE cc_start: 0.8315 (mm) cc_final: 0.8112 (mp) REVERT: F 169 HIS cc_start: 0.8086 (t-90) cc_final: 0.7867 (t-90) REVERT: F 177 ASN cc_start: 0.8231 (t0) cc_final: 0.7900 (t0) REVERT: F 178 LEU cc_start: 0.8848 (tp) cc_final: 0.8530 (tp) REVERT: F 239 THR cc_start: 0.8018 (m) cc_final: 0.7791 (m) REVERT: F 274 ARG cc_start: 0.7878 (tmm160) cc_final: 0.7296 (tmm160) REVERT: F 276 MET cc_start: 0.9135 (tpp) cc_final: 0.8568 (tpp) REVERT: A 165 LYS cc_start: 0.7715 (tmtt) cc_final: 0.7350 (tmtt) REVERT: A 177 ASN cc_start: 0.6187 (t0) cc_final: 0.5940 (t0) REVERT: A 179 HIS cc_start: 0.6849 (m-70) cc_final: 0.6504 (m-70) REVERT: A 333 MET cc_start: 0.8670 (ttm) cc_final: 0.8411 (tmm) REVERT: C 227 HIS cc_start: 0.6600 (t-90) cc_final: 0.6265 (t-90) REVERT: E 238 MET cc_start: 0.7677 (ptt) cc_final: 0.7427 (ptt) outliers start: 32 outliers final: 24 residues processed: 222 average time/residue: 0.2555 time to fit residues: 81.6419 Evaluate side-chains 213 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 157 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.0070 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 179 HIS ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13314 Z= 0.186 Angle : 0.756 13.604 18018 Z= 0.352 Chirality : 0.045 0.200 2042 Planarity : 0.006 0.093 2325 Dihedral : 8.175 120.045 1871 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.88 % Allowed : 16.86 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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 (0.20), residues: 1618 helix: -0.62 (0.19), residues: 726 sheet: -1.61 (0.42), residues: 149 loop : -2.50 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 241 HIS 0.015 0.001 HIS F 179 PHE 0.029 0.002 PHE A 175 TYR 0.014 0.001 TYR B 129 ARG 0.008 0.000 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8910 (m-80) cc_final: 0.8524 (m-80) REVERT: F 169 HIS cc_start: 0.8110 (t-90) cc_final: 0.7879 (t-90) REVERT: F 177 ASN cc_start: 0.8217 (t0) cc_final: 0.7928 (t0) REVERT: F 178 LEU cc_start: 0.8864 (tp) cc_final: 0.8578 (tp) REVERT: F 276 MET cc_start: 0.9176 (tpp) cc_final: 0.8882 (tpp) REVERT: A 165 LYS cc_start: 0.7717 (tttt) cc_final: 0.7300 (tmtt) REVERT: A 179 HIS cc_start: 0.6873 (m-70) cc_final: 0.6618 (m-70) REVERT: A 276 MET cc_start: 0.6079 (ppp) cc_final: 0.5866 (pmm) REVERT: A 333 MET cc_start: 0.8690 (ttm) cc_final: 0.8469 (tmm) REVERT: B 58 ARG cc_start: 0.7936 (ttm110) cc_final: 0.7464 (tpp-160) REVERT: E 133 MET cc_start: 0.8484 (ppp) cc_final: 0.8081 (ppp) outliers start: 40 outliers final: 29 residues processed: 224 average time/residue: 0.2524 time to fit residues: 81.5569 Evaluate side-chains 209 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS B 177 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 254 ASN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13314 Z= 0.248 Angle : 0.786 14.538 18018 Z= 0.368 Chirality : 0.046 0.190 2042 Planarity : 0.006 0.097 2325 Dihedral : 8.155 118.978 1871 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.25 % Favored : 88.69 % Rotamer: Outliers : 2.88 % Allowed : 18.66 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -2.37 (0.21), residues: 1618 helix: -0.72 (0.19), residues: 739 sheet: -1.53 (0.43), residues: 144 loop : -2.48 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 241 HIS 0.015 0.001 HIS F 179 PHE 0.029 0.002 PHE A 175 TYR 0.038 0.001 TYR A 129 ARG 0.008 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8939 (m-80) cc_final: 0.8454 (m-80) REVERT: F 169 HIS cc_start: 0.8164 (t-90) cc_final: 0.7925 (t-90) REVERT: F 177 ASN cc_start: 0.8217 (t0) cc_final: 0.7967 (t0) REVERT: F 178 LEU cc_start: 0.8864 (tp) cc_final: 0.8585 (tp) REVERT: F 239 THR cc_start: 0.7894 (m) cc_final: 0.7690 (m) REVERT: F 269 ASP cc_start: 0.6654 (t0) cc_final: 0.6101 (m-30) REVERT: F 276 MET cc_start: 0.9205 (tpp) cc_final: 0.8989 (tpp) REVERT: A 165 LYS cc_start: 0.7681 (tttt) cc_final: 0.7338 (tmtt) REVERT: A 179 HIS cc_start: 0.6775 (m-70) cc_final: 0.6425 (m-70) REVERT: A 333 MET cc_start: 0.8701 (ttm) cc_final: 0.8482 (tmm) REVERT: B 58 ARG cc_start: 0.7997 (ttm110) cc_final: 0.7505 (tpp-160) REVERT: C 227 HIS cc_start: 0.6710 (t-90) cc_final: 0.6393 (t-90) REVERT: E 133 MET cc_start: 0.8510 (ppp) cc_final: 0.8144 (ppp) outliers start: 40 outliers final: 30 residues processed: 214 average time/residue: 0.2674 time to fit residues: 84.4423 Evaluate side-chains 204 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN D 54 GLN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13314 Z= 0.223 Angle : 0.784 16.470 18018 Z= 0.367 Chirality : 0.046 0.214 2042 Planarity : 0.006 0.093 2325 Dihedral : 8.108 118.779 1871 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.00 % Favored : 88.94 % Rotamer: Outliers : 2.74 % Allowed : 19.16 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -2.29 (0.21), residues: 1618 helix: -0.63 (0.19), residues: 742 sheet: -1.60 (0.42), residues: 145 loop : -2.45 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 241 HIS 0.006 0.001 HIS F 179 PHE 0.032 0.002 PHE A 175 TYR 0.032 0.001 TYR A 129 ARG 0.008 0.000 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8931 (m-80) cc_final: 0.8714 (m-80) REVERT: F 169 HIS cc_start: 0.8195 (t-90) cc_final: 0.7937 (t-90) REVERT: F 177 ASN cc_start: 0.8289 (t0) cc_final: 0.8019 (t0) REVERT: F 178 LEU cc_start: 0.8854 (tp) cc_final: 0.8575 (tp) REVERT: F 269 ASP cc_start: 0.6734 (t0) cc_final: 0.6399 (m-30) REVERT: F 276 MET cc_start: 0.9228 (tpp) cc_final: 0.8862 (tpp) REVERT: A 123 LEU cc_start: 0.9366 (mt) cc_final: 0.9164 (mp) REVERT: A 165 LYS cc_start: 0.7683 (tttt) cc_final: 0.7328 (tmtt) REVERT: A 179 HIS cc_start: 0.6767 (m-70) cc_final: 0.6530 (m-70) REVERT: A 333 MET cc_start: 0.8695 (ttm) cc_final: 0.8473 (tmm) REVERT: B 54 GLN cc_start: 0.9208 (mt0) cc_final: 0.8825 (mm110) REVERT: B 58 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7524 (tpp-160) REVERT: C 203 LYS cc_start: 0.8554 (tttt) cc_final: 0.8340 (ttmm) REVERT: E 133 MET cc_start: 0.8482 (ppp) cc_final: 0.8166 (ppp) outliers start: 38 outliers final: 30 residues processed: 215 average time/residue: 0.2622 time to fit residues: 80.6291 Evaluate side-chains 211 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13314 Z= 0.233 Angle : 0.801 16.464 18018 Z= 0.376 Chirality : 0.046 0.238 2042 Planarity : 0.006 0.093 2325 Dihedral : 8.083 117.940 1871 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.00 % Favored : 88.94 % Rotamer: Outliers : 2.59 % Allowed : 20.24 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -2.26 (0.21), residues: 1618 helix: -0.60 (0.19), residues: 740 sheet: -1.60 (0.42), residues: 145 loop : -2.42 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 241 HIS 0.005 0.001 HIS B 227 PHE 0.031 0.002 PHE A 175 TYR 0.035 0.001 TYR A 129 ARG 0.017 0.000 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8918 (m-80) cc_final: 0.8681 (m-80) REVERT: F 169 HIS cc_start: 0.8215 (t-90) cc_final: 0.7951 (t-90) REVERT: F 177 ASN cc_start: 0.8259 (t0) cc_final: 0.8002 (t0) REVERT: F 178 LEU cc_start: 0.8882 (tp) cc_final: 0.8603 (tp) REVERT: F 269 ASP cc_start: 0.6700 (t0) cc_final: 0.6420 (m-30) REVERT: F 276 MET cc_start: 0.9223 (tpp) cc_final: 0.8960 (tpp) REVERT: A 165 LYS cc_start: 0.7666 (tttt) cc_final: 0.7310 (tmtt) REVERT: A 179 HIS cc_start: 0.6872 (m-70) cc_final: 0.6608 (m-70) REVERT: A 333 MET cc_start: 0.8713 (ttm) cc_final: 0.8496 (tmm) REVERT: B 58 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7530 (tpp-160) REVERT: B 136 LEU cc_start: 0.8312 (pp) cc_final: 0.7956 (mp) REVERT: C 203 LYS cc_start: 0.8571 (tttt) cc_final: 0.8366 (ttmm) REVERT: E 133 MET cc_start: 0.8446 (ppp) cc_final: 0.8122 (ppp) outliers start: 36 outliers final: 29 residues processed: 207 average time/residue: 0.2488 time to fit residues: 74.2756 Evaluate side-chains 208 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN D 227 HIS ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13314 Z= 0.216 Angle : 0.814 17.862 18018 Z= 0.376 Chirality : 0.046 0.224 2042 Planarity : 0.006 0.092 2325 Dihedral : 8.019 117.623 1871 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.88 % Allowed : 20.24 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -2.21 (0.21), residues: 1618 helix: -0.55 (0.19), residues: 733 sheet: -1.58 (0.42), residues: 147 loop : -2.39 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 241 HIS 0.005 0.001 HIS B 227 PHE 0.032 0.002 PHE A 175 TYR 0.028 0.001 TYR A 129 ARG 0.011 0.000 ARG F 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8890 (m-80) cc_final: 0.8644 (m-80) REVERT: F 169 HIS cc_start: 0.8118 (t-90) cc_final: 0.7851 (t-90) REVERT: F 177 ASN cc_start: 0.8225 (t0) cc_final: 0.7949 (t0) REVERT: F 178 LEU cc_start: 0.8854 (tp) cc_final: 0.8565 (tp) REVERT: F 276 MET cc_start: 0.9176 (tpp) cc_final: 0.8917 (tpp) REVERT: A 165 LYS cc_start: 0.7655 (tttt) cc_final: 0.7306 (tmtt) REVERT: A 179 HIS cc_start: 0.6856 (m-70) cc_final: 0.6590 (m-70) REVERT: B 58 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7525 (tpp-160) REVERT: B 136 LEU cc_start: 0.8333 (pp) cc_final: 0.7971 (mp) REVERT: C 203 LYS cc_start: 0.8557 (tttt) cc_final: 0.8342 (ttmm) REVERT: C 227 HIS cc_start: 0.6594 (t-90) cc_final: 0.6284 (t-90) REVERT: D 196 ARG cc_start: 0.8207 (ptm-80) cc_final: 0.7967 (ttp80) REVERT: E 133 MET cc_start: 0.8432 (ppp) cc_final: 0.8177 (ppp) outliers start: 40 outliers final: 31 residues processed: 212 average time/residue: 0.2644 time to fit residues: 79.8051 Evaluate side-chains 207 residues out of total 1389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.123395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.093131 restraints weight = 36329.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094605 restraints weight = 25257.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.094771 restraints weight = 18374.072| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13314 Z= 0.289 Angle : 0.855 16.281 18018 Z= 0.395 Chirality : 0.047 0.214 2042 Planarity : 0.006 0.094 2325 Dihedral : 8.082 117.476 1871 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.74 % Favored : 88.20 % Rotamer: Outliers : 2.74 % Allowed : 20.89 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % 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: -2.30 (0.21), residues: 1618 helix: -0.68 (0.19), residues: 746 sheet: -1.55 (0.43), residues: 144 loop : -2.42 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 241 HIS 0.005 0.001 HIS B 227 PHE 0.031 0.002 PHE A 175 TYR 0.024 0.001 TYR A 129 ARG 0.014 0.001 ARG A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2710.55 seconds wall clock time: 49 minutes 48.19 seconds (2988.19 seconds total)