Starting phenix.real_space_refine on Fri Feb 16 11:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2s_15105/02_2024/8a2s_15105_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2s_15105/02_2024/8a2s_15105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2s_15105/02_2024/8a2s_15105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2s_15105/02_2024/8a2s_15105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2s_15105/02_2024/8a2s_15105_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2s_15105/02_2024/8a2s_15105_updated.pdb" } resolution = 2.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 9170 2.51 5 N 2450 2.21 5 O 3401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15141 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 145 Classifications: {'water': 145} Link IDs: {None: 144} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "E" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Time building chain proxies: 8.44, per 1000 atoms: 0.56 Number of scatterers: 15141 At special positions: 0 Unit cell: (94.52, 87.57, 193.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 15 15.00 Mg 5 11.99 O 3401 8.00 N 2450 7.00 C 9170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 2.8 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 20 sheets defined 45.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.690A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.563A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 294 removed outlier: 5.047A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.371A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.532A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.847A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.690A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.563A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 287 through 294 removed outlier: 5.047A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.370A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.533A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 354' Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.848A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.690A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.563A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 294 removed outlier: 5.047A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.371A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.533A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 354' Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.848A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.690A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.563A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 287 through 294 removed outlier: 5.047A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.370A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.533A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 354' Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.848A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.690A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.563A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 287 through 294 removed outlier: 5.047A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.371A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.533A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 350 through 354' Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.848A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.579A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.287A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.579A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.288A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.580A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.287A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.580A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.287A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.578A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.287A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 530 hydrogen bonds defined for protein. 1260 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: 4.84 Time building geometry restraints manager: 7.33 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: 4520 1.33 - 1.45: 2105 1.45 - 1.57: 8045 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14860 Sorted by residual: bond pdb=" O4 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.491 0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O4 PO4 D 403 " pdb=" P PO4 D 403 " ideal model delta sigma weight residual 1.568 1.492 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.492 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 14855 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.01: 600 107.01 - 114.41: 8642 114.41 - 121.81: 7828 121.81 - 129.21: 3005 129.21 - 136.61: 95 Bond angle restraints: 20170 Sorted by residual: angle pdb=" PA ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sigma weight residual 120.50 128.48 -7.98 3.00e+00 1.11e-01 7.07e+00 angle pdb=" PA ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sigma weight residual 120.50 128.46 -7.96 3.00e+00 1.11e-01 7.04e+00 angle pdb=" PA ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sigma weight residual 120.50 128.43 -7.93 3.00e+00 1.11e-01 6.98e+00 angle pdb=" PA ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sigma weight residual 120.50 128.42 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" PA ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sigma weight residual 120.50 128.42 -7.92 3.00e+00 1.11e-01 6.96e+00 ... (remaining 20165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 8780 35.96 - 71.92: 130 71.92 - 107.88: 10 107.88 - 143.85: 5 143.85 - 179.81: 5 Dihedral angle restraints: 8930 sinusoidal: 3615 harmonic: 5315 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.19 179.81 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.21 179.79 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 120.21 179.79 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1187 0.040 - 0.080: 750 0.080 - 0.120: 269 0.120 - 0.161: 29 0.161 - 0.201: 5 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 2237 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " 0.021 2.00e-02 2.50e+03 1.04e-02 2.70e+00 pdb=" CG TRP B 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " 0.021 2.00e-02 2.50e+03 1.04e-02 2.68e+00 pdb=" CG TRP D 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 340 " 0.021 2.00e-02 2.50e+03 1.03e-02 2.68e+00 pdb=" CG TRP C 340 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP C 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP C 340 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 340 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 340 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 340 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 340 " 0.004 2.00e-02 2.50e+03 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 92 2.39 - 3.01: 8499 3.01 - 3.64: 24506 3.64 - 4.27: 42178 4.27 - 4.90: 64241 Nonbonded interactions: 139516 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 506 " model vdw 1.758 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 515 " model vdw 1.780 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 559 " model vdw 1.800 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 527 " model vdw 1.851 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 526 " model vdw 1.860 2.170 ... (remaining 139511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 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: 12.240 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 43.810 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 0.009 0.077 14860 Z= 0.582 Angle : 0.677 7.978 20170 Z= 0.338 Chirality : 0.053 0.201 2240 Planarity : 0.005 0.044 2570 Dihedral : 14.102 179.806 5520 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.64 % Allowed : 3.22 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1800 helix: -2.19 (0.14), residues: 775 sheet: -0.30 (0.25), residues: 330 loop : 1.26 (0.26), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 340 HIS 0.005 0.002 HIS B 173 PHE 0.016 0.002 PHE B 262 TYR 0.008 0.002 TYR A 143 ARG 0.006 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 1.909 Fit side-chains REVERT: C 28 ARG cc_start: 0.8243 (ttm170) cc_final: 0.8026 (ttm170) REVERT: C 121 GLN cc_start: 0.8463 (tt0) cc_final: 0.8258 (tt0) REVERT: A 44 MET cc_start: 0.8413 (mmm) cc_final: 0.8201 (mmt) REVERT: A 191 LYS cc_start: 0.8441 (tttm) cc_final: 0.8200 (ttmm) REVERT: B 41 GLN cc_start: 0.7252 (tt0) cc_final: 0.6595 (tp-100) REVERT: B 64 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8587 (pp) REVERT: B 121 GLN cc_start: 0.8331 (tt0) cc_final: 0.8075 (tt0) REVERT: B 125 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 211 ASP cc_start: 0.7917 (t70) cc_final: 0.7637 (t70) REVERT: B 355 MET cc_start: 0.8207 (mmm) cc_final: 0.7962 (mmm) REVERT: D 41 GLN cc_start: 0.6948 (tt0) cc_final: 0.6351 (tp-100) REVERT: D 57 GLU cc_start: 0.7397 (tt0) cc_final: 0.7118 (mt-10) REVERT: D 128 ASN cc_start: 0.7942 (m110) cc_final: 0.7678 (t0) REVERT: E 50 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7528 (mtpt) REVERT: E 214 GLU cc_start: 0.8210 (mt-10) cc_final: 0.8000 (mt-10) outliers start: 10 outliers final: 5 residues processed: 272 average time/residue: 1.5416 time to fit residues: 455.5077 Evaluate side-chains 202 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 225 ASN A 314 GLN A 353 GLN B 246 GLN E 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14860 Z= 0.157 Angle : 0.561 6.585 20170 Z= 0.269 Chirality : 0.045 0.154 2240 Planarity : 0.004 0.027 2570 Dihedral : 10.901 162.765 2068 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.74 % Allowed : 9.07 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1800 helix: -0.74 (0.17), residues: 795 sheet: -0.21 (0.25), residues: 335 loop : 1.77 (0.27), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS C 161 PHE 0.011 0.001 PHE C 255 TYR 0.010 0.001 TYR B 143 ARG 0.006 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 1.933 Fit side-chains REVERT: C 28 ARG cc_start: 0.8224 (ttm170) cc_final: 0.8012 (ttm170) REVERT: A 64 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9099 (pp) REVERT: A 66 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8520 (m) REVERT: A 191 LYS cc_start: 0.8390 (tttm) cc_final: 0.8136 (ttmm) REVERT: B 41 GLN cc_start: 0.7270 (tt0) cc_final: 0.6610 (tp-100) REVERT: B 211 ASP cc_start: 0.7869 (t70) cc_final: 0.7614 (t70) REVERT: B 351 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8137 (p) REVERT: B 355 MET cc_start: 0.8185 (mmm) cc_final: 0.7952 (mmm) REVERT: D 41 GLN cc_start: 0.6946 (tt0) cc_final: 0.6334 (tp40) REVERT: D 57 GLU cc_start: 0.7380 (tt0) cc_final: 0.7137 (mt-10) REVERT: D 128 ASN cc_start: 0.7925 (m110) cc_final: 0.7702 (t0) REVERT: E 50 LYS cc_start: 0.7848 (mtmm) cc_final: 0.7592 (mtpt) REVERT: E 64 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8358 (pp) REVERT: E 66 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8221 (m) REVERT: E 214 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7881 (mt-10) outliers start: 27 outliers final: 8 residues processed: 224 average time/residue: 1.6241 time to fit residues: 394.8735 Evaluate side-chains 204 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN A 353 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14860 Z= 0.337 Angle : 0.631 7.050 20170 Z= 0.308 Chirality : 0.049 0.172 2240 Planarity : 0.004 0.033 2570 Dihedral : 11.134 177.115 2062 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.51 % Allowed : 10.55 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1800 helix: -0.42 (0.18), residues: 795 sheet: -0.08 (0.26), residues: 325 loop : 1.81 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 340 HIS 0.005 0.002 HIS C 173 PHE 0.016 0.002 PHE D 262 TYR 0.009 0.001 TYR A 143 ARG 0.006 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.742 Fit side-chains REVERT: C 125 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: A 28 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7843 (ttm170) REVERT: A 64 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9085 (pp) REVERT: A 66 THR cc_start: 0.8768 (t) cc_final: 0.8566 (m) REVERT: A 191 LYS cc_start: 0.8419 (tttm) cc_final: 0.8177 (ttmm) REVERT: B 41 GLN cc_start: 0.7277 (tt0) cc_final: 0.6614 (tp40) REVERT: B 125 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: B 355 MET cc_start: 0.8250 (mmm) cc_final: 0.7966 (mmm) REVERT: D 41 GLN cc_start: 0.6926 (tt0) cc_final: 0.6296 (tp40) REVERT: D 57 GLU cc_start: 0.7442 (tt0) cc_final: 0.7174 (mt-10) REVERT: D 64 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8513 (pp) REVERT: D 125 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: D 128 ASN cc_start: 0.7928 (m110) cc_final: 0.7673 (t0) REVERT: D 276 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: D 355 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7192 (mtp) REVERT: E 50 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7582 (mtpt) REVERT: E 64 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8395 (pp) REVERT: E 95 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.7148 (mtt180) REVERT: E 214 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7899 (mt-10) outliers start: 39 outliers final: 15 residues processed: 220 average time/residue: 1.5201 time to fit residues: 363.7234 Evaluate side-chains 210 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN A 225 ASN A 353 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14860 Z= 0.243 Angle : 0.583 6.739 20170 Z= 0.280 Chirality : 0.047 0.168 2240 Planarity : 0.004 0.031 2570 Dihedral : 10.586 179.672 2062 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.57 % Allowed : 11.25 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1800 helix: -0.26 (0.18), residues: 795 sheet: 0.00 (0.27), residues: 325 loop : 1.86 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 79 HIS 0.004 0.001 HIS D 173 PHE 0.013 0.001 PHE D 262 TYR 0.008 0.001 TYR A 143 ARG 0.004 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.958 Fit side-chains REVERT: C 125 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: C 360 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7225 (mp-120) REVERT: A 64 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9105 (pp) REVERT: A 84 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8466 (mttm) REVERT: A 191 LYS cc_start: 0.8408 (tttm) cc_final: 0.8159 (ttmm) REVERT: B 41 GLN cc_start: 0.7286 (tt0) cc_final: 0.6616 (tp40) REVERT: B 125 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: B 355 MET cc_start: 0.8244 (mmm) cc_final: 0.7977 (mmm) REVERT: D 41 GLN cc_start: 0.6907 (tt0) cc_final: 0.6269 (tp40) REVERT: D 57 GLU cc_start: 0.7428 (tt0) cc_final: 0.7179 (mt-10) REVERT: D 128 ASN cc_start: 0.7936 (m110) cc_final: 0.7679 (t0) REVERT: D 355 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7229 (mtp) REVERT: E 50 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7556 (mtpt) REVERT: E 64 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8373 (pp) REVERT: E 95 ARG cc_start: 0.7416 (mtt-85) cc_final: 0.7196 (mtt90) REVERT: E 214 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7897 (mt-10) REVERT: E 215 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8080 (mppt) REVERT: E 355 MET cc_start: 0.7995 (mmm) cc_final: 0.7684 (mtp) outliers start: 40 outliers final: 18 residues processed: 215 average time/residue: 1.5948 time to fit residues: 372.9666 Evaluate side-chains 210 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN A 225 ASN A 353 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14860 Z= 0.306 Angle : 0.615 6.921 20170 Z= 0.298 Chirality : 0.048 0.175 2240 Planarity : 0.004 0.031 2570 Dihedral : 10.834 172.437 2062 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.57 % Allowed : 11.38 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1800 helix: -0.24 (0.18), residues: 795 sheet: 0.01 (0.27), residues: 325 loop : 1.85 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 340 HIS 0.005 0.001 HIS C 173 PHE 0.015 0.002 PHE D 262 TYR 0.007 0.001 TYR D 166 ARG 0.004 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 1.954 Fit side-chains REVERT: C 125 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: C 360 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7226 (mp-120) REVERT: A 64 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9104 (pp) REVERT: A 84 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8500 (mttm) REVERT: A 191 LYS cc_start: 0.8418 (tttm) cc_final: 0.8172 (ttmm) REVERT: B 41 GLN cc_start: 0.7287 (tt0) cc_final: 0.6621 (tp40) REVERT: B 64 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8478 (pp) REVERT: B 355 MET cc_start: 0.8261 (mmm) cc_final: 0.7966 (mmm) REVERT: D 41 GLN cc_start: 0.6906 (tt0) cc_final: 0.6272 (tp40) REVERT: D 57 GLU cc_start: 0.7422 (tt0) cc_final: 0.7172 (mt-10) REVERT: D 64 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8520 (pp) REVERT: D 125 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: D 128 ASN cc_start: 0.7934 (m110) cc_final: 0.7658 (t0) REVERT: D 355 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7240 (mtp) REVERT: E 50 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7565 (mtpt) REVERT: E 64 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8396 (pp) REVERT: E 95 ARG cc_start: 0.7428 (mtt-85) cc_final: 0.7209 (mtt90) REVERT: E 214 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7904 (mt-10) REVERT: E 215 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8043 (mtpt) REVERT: E 355 MET cc_start: 0.7997 (mmm) cc_final: 0.7674 (mtp) outliers start: 40 outliers final: 22 residues processed: 213 average time/residue: 1.5563 time to fit residues: 361.0183 Evaluate side-chains 216 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN A 353 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14860 Z= 0.258 Angle : 0.589 6.745 20170 Z= 0.284 Chirality : 0.047 0.172 2240 Planarity : 0.004 0.031 2570 Dihedral : 10.529 175.144 2062 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.64 % Allowed : 11.70 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1800 helix: -0.19 (0.18), residues: 795 sheet: 0.04 (0.27), residues: 325 loop : 1.89 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 340 HIS 0.004 0.001 HIS C 173 PHE 0.013 0.001 PHE D 262 TYR 0.007 0.001 TYR A 143 ARG 0.006 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 192 time to evaluate : 1.744 Fit side-chains REVERT: C 125 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: C 360 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7220 (mp-120) REVERT: A 64 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9106 (pp) REVERT: A 84 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8479 (mttm) REVERT: A 191 LYS cc_start: 0.8415 (tttm) cc_final: 0.8163 (ttmm) REVERT: A 355 MET cc_start: 0.8301 (mmm) cc_final: 0.7927 (mmm) REVERT: B 41 GLN cc_start: 0.7278 (tt0) cc_final: 0.6611 (tp40) REVERT: B 64 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8476 (pp) REVERT: B 95 ARG cc_start: 0.7603 (mtt-85) cc_final: 0.7364 (mtp85) REVERT: B 125 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: B 355 MET cc_start: 0.8247 (mmm) cc_final: 0.7975 (mmm) REVERT: D 41 GLN cc_start: 0.6909 (tt0) cc_final: 0.6280 (tp40) REVERT: D 57 GLU cc_start: 0.7402 (tt0) cc_final: 0.7159 (mt-10) REVERT: D 64 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8527 (pp) REVERT: D 128 ASN cc_start: 0.7941 (m110) cc_final: 0.7660 (t0) REVERT: D 355 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7220 (mtp) REVERT: E 50 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7555 (mtpt) REVERT: E 64 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8378 (pp) REVERT: E 95 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.7208 (mtt90) REVERT: E 214 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7888 (mt-10) REVERT: E 215 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8082 (mppt) REVERT: E 355 MET cc_start: 0.7983 (mmm) cc_final: 0.7648 (mtp) outliers start: 41 outliers final: 22 residues processed: 218 average time/residue: 1.5921 time to fit residues: 377.0431 Evaluate side-chains 220 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN A 353 GLN B 225 ASN E 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14860 Z= 0.166 Angle : 0.545 6.621 20170 Z= 0.257 Chirality : 0.045 0.158 2240 Planarity : 0.003 0.033 2570 Dihedral : 9.744 171.479 2062 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.12 % Allowed : 12.41 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1800 helix: -0.01 (0.19), residues: 785 sheet: 0.11 (0.27), residues: 325 loop : 1.85 (0.27), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.006 0.001 HIS E 87 PHE 0.010 0.001 PHE E 31 TYR 0.007 0.001 TYR C 143 ARG 0.008 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.830 Fit side-chains REVERT: C 125 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: C 360 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7180 (mp-120) REVERT: A 64 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9104 (pp) REVERT: A 84 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8414 (mttm) REVERT: A 191 LYS cc_start: 0.8391 (tttm) cc_final: 0.8127 (ttmm) REVERT: A 355 MET cc_start: 0.8285 (mmm) cc_final: 0.7915 (mmm) REVERT: B 41 GLN cc_start: 0.7257 (tt0) cc_final: 0.6585 (tp40) REVERT: B 355 MET cc_start: 0.8219 (mmm) cc_final: 0.7970 (mmm) REVERT: D 41 GLN cc_start: 0.6906 (tt0) cc_final: 0.6280 (tp40) REVERT: D 57 GLU cc_start: 0.7386 (tt0) cc_final: 0.7141 (mt-10) REVERT: D 128 ASN cc_start: 0.7924 (m110) cc_final: 0.7644 (t0) REVERT: D 355 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7254 (mtp) REVERT: E 25 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7240 (p0) REVERT: E 50 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7551 (mtpt) REVERT: E 64 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8373 (pp) REVERT: E 95 ARG cc_start: 0.7374 (mtt-85) cc_final: 0.7154 (mtt180) REVERT: E 215 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8044 (mppt) REVERT: E 355 MET cc_start: 0.7954 (mmm) cc_final: 0.7660 (mtp) outliers start: 33 outliers final: 18 residues processed: 212 average time/residue: 1.5820 time to fit residues: 364.2110 Evaluate side-chains 215 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 354 GLN A 353 GLN B 40 HIS B 225 ASN B 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14860 Z= 0.204 Angle : 0.564 6.586 20170 Z= 0.268 Chirality : 0.046 0.163 2240 Planarity : 0.004 0.031 2570 Dihedral : 9.614 171.837 2060 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.93 % Allowed : 12.86 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1800 helix: -0.00 (0.19), residues: 785 sheet: 0.14 (0.27), residues: 325 loop : 1.86 (0.27), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.003 0.001 HIS E 161 PHE 0.011 0.001 PHE D 262 TYR 0.007 0.001 TYR A 143 ARG 0.006 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 1.956 Fit side-chains REVERT: C 125 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: C 360 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7179 (mp-120) REVERT: A 64 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9097 (pp) REVERT: A 84 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8444 (mttm) REVERT: A 191 LYS cc_start: 0.8399 (tttm) cc_final: 0.8138 (ttmm) REVERT: A 355 MET cc_start: 0.8270 (mmm) cc_final: 0.7881 (mmm) REVERT: B 41 GLN cc_start: 0.7250 (tt0) cc_final: 0.6582 (tp40) REVERT: B 44 MET cc_start: 0.8663 (mtp) cc_final: 0.8174 (mtp) REVERT: B 125 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: B 355 MET cc_start: 0.8224 (mmm) cc_final: 0.7976 (mmm) REVERT: D 41 GLN cc_start: 0.6903 (tt0) cc_final: 0.6283 (tp40) REVERT: D 57 GLU cc_start: 0.7418 (tt0) cc_final: 0.7178 (mt-10) REVERT: D 128 ASN cc_start: 0.7913 (m110) cc_final: 0.7635 (t0) REVERT: D 355 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7254 (mtp) REVERT: E 25 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7244 (p0) REVERT: E 50 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7552 (mtpt) REVERT: E 64 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8380 (pp) REVERT: E 95 ARG cc_start: 0.7389 (mtt-85) cc_final: 0.7167 (mtt180) REVERT: E 215 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8053 (mppt) REVERT: E 355 MET cc_start: 0.7976 (mmm) cc_final: 0.7656 (mtp) outliers start: 30 outliers final: 17 residues processed: 207 average time/residue: 1.6260 time to fit residues: 366.6639 Evaluate side-chains 215 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.4980 chunk 166 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 0.0980 chunk 106 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN A 40 HIS A 353 GLN B 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14860 Z= 0.136 Angle : 0.526 6.821 20170 Z= 0.246 Chirality : 0.044 0.144 2240 Planarity : 0.003 0.034 2570 Dihedral : 8.869 159.015 2060 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.74 % Allowed : 12.99 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1800 helix: 0.19 (0.19), residues: 775 sheet: 0.23 (0.27), residues: 325 loop : 1.79 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.003 0.001 HIS D 101 PHE 0.010 0.001 PHE E 31 TYR 0.007 0.001 TYR C 143 ARG 0.006 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.903 Fit side-chains REVERT: C 125 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: C 328 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8160 (tttt) REVERT: C 360 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7192 (mp-120) REVERT: A 64 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9110 (pp) REVERT: A 191 LYS cc_start: 0.8373 (tttm) cc_final: 0.8110 (ttmm) REVERT: A 355 MET cc_start: 0.8253 (mmm) cc_final: 0.7887 (mmm) REVERT: B 41 GLN cc_start: 0.7236 (tt0) cc_final: 0.6577 (tp40) REVERT: B 351 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8134 (p) REVERT: B 355 MET cc_start: 0.8184 (mmm) cc_final: 0.7956 (mmm) REVERT: D 41 GLN cc_start: 0.6908 (tt0) cc_final: 0.6293 (tp40) REVERT: D 57 GLU cc_start: 0.7391 (tt0) cc_final: 0.7158 (mt-10) REVERT: D 128 ASN cc_start: 0.7901 (m110) cc_final: 0.7641 (t0) REVERT: D 355 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7273 (mtp) REVERT: E 50 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7550 (mtpt) REVERT: E 64 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8369 (pp) REVERT: E 117 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7487 (mt-10) REVERT: E 125 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6841 (mt-10) REVERT: E 215 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7998 (mppt) REVERT: E 355 MET cc_start: 0.7943 (mmm) cc_final: 0.7662 (mtp) outliers start: 27 outliers final: 13 residues processed: 208 average time/residue: 1.5132 time to fit residues: 343.3610 Evaluate side-chains 207 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 323 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN A 353 GLN B 246 GLN E 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14860 Z= 0.218 Angle : 0.568 6.821 20170 Z= 0.270 Chirality : 0.046 0.162 2240 Planarity : 0.004 0.031 2570 Dihedral : 9.154 165.177 2060 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.61 % Allowed : 13.50 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1800 helix: 0.15 (0.19), residues: 775 sheet: 0.22 (0.27), residues: 325 loop : 1.81 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.007 0.001 HIS E 87 PHE 0.011 0.001 PHE D 262 TYR 0.007 0.001 TYR D 69 ARG 0.006 0.000 ARG D 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.844 Fit side-chains REVERT: C 125 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: C 360 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7191 (mp-120) REVERT: A 64 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9098 (pp) REVERT: A 191 LYS cc_start: 0.8406 (tttm) cc_final: 0.8148 (ttmm) REVERT: A 355 MET cc_start: 0.8273 (mmm) cc_final: 0.7909 (mmm) REVERT: B 41 GLN cc_start: 0.7187 (tt0) cc_final: 0.6543 (tp40) REVERT: B 351 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8144 (p) REVERT: B 355 MET cc_start: 0.8208 (mmm) cc_final: 0.7984 (mmm) REVERT: D 41 GLN cc_start: 0.6909 (tt0) cc_final: 0.6291 (tp40) REVERT: D 57 GLU cc_start: 0.7411 (tt0) cc_final: 0.7158 (mt-10) REVERT: D 128 ASN cc_start: 0.7914 (m110) cc_final: 0.7633 (t0) REVERT: D 355 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7237 (mtp) REVERT: E 25 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7232 (p0) REVERT: E 50 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7554 (mtpt) REVERT: E 64 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8385 (pp) REVERT: E 95 ARG cc_start: 0.7370 (mtt-85) cc_final: 0.7160 (mtt180) REVERT: E 125 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6843 (mt-10) REVERT: E 215 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8034 (mppt) REVERT: E 355 MET cc_start: 0.7958 (mmm) cc_final: 0.7663 (mtp) outliers start: 25 outliers final: 15 residues processed: 201 average time/residue: 1.5440 time to fit residues: 337.9761 Evaluate side-chains 209 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN B 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.098123 restraints weight = 15067.961| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.17 r_work: 0.2972 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14860 Z= 0.290 Angle : 0.608 6.935 20170 Z= 0.293 Chirality : 0.048 0.176 2240 Planarity : 0.004 0.032 2570 Dihedral : 9.781 178.033 2060 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.61 % Allowed : 13.50 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1800 helix: -0.07 (0.18), residues: 790 sheet: 0.13 (0.27), residues: 325 loop : 1.89 (0.27), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 340 HIS 0.005 0.001 HIS C 173 PHE 0.015 0.002 PHE D 262 TYR 0.008 0.001 TYR D 69 ARG 0.006 0.001 ARG D 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6319.83 seconds wall clock time: 113 minutes 14.91 seconds (6794.91 seconds total)