Starting phenix.real_space_refine on Sat Mar 16 16:26:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2u_15107/03_2024/8a2u_15107_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2u_15107/03_2024/8a2u_15107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2u_15107/03_2024/8a2u_15107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2u_15107/03_2024/8a2u_15107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2u_15107/03_2024/8a2u_15107_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2u_15107/03_2024/8a2u_15107_updated.pdb" } resolution = 2.21 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 10 5.49 5 S 100 5.16 5 Be 5 3.05 5 C 9145 2.51 5 N 2445 2.21 5 O 3297 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15022 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} 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: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} 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: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} 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: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} 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: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Time building chain proxies: 8.52, per 1000 atoms: 0.57 Number of scatterers: 15022 At special positions: 0 Unit cell: (93.825, 89.655, 192.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 S 100 16.00 P 10 15.00 F 15 9.00 O 3297 8.00 N 2445 7.00 C 9145 6.00 Be 5 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.12 Conformation dependent library (CDL) restraints added in 2.7 seconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 20 sheets defined 43.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 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: 3.733A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.460A 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 230 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.587A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.589A 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: 3.533A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.523A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.580A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 370 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: 3.733A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.460A 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 230 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.587A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.589A 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: 3.533A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.523A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 removed outlier: 3.579A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 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: 3.732A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.460A 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 230 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.587A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.589A 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: 3.532A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.523A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.579A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 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: 3.733A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.460A 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 230 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.586A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.589A 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: 3.532A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.522A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.579A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 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: 3.733A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.461A 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 230 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.586A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.589A 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: 3.533A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.524A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 removed outlier: 3.580A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 370 Processing sheet with id= A, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.626A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= C, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.296A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.206A 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: 6.626A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 65 through 69 Processing sheet with id= G, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.296A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.205A 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: 6.626A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 65 through 69 Processing sheet with id= K, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.296A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.206A 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: 6.627A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 65 through 69 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.296A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.205A 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: 6.626A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 65 through 69 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.295A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.205A 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. 1275 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: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4702 1.34 - 1.46: 3040 1.46 - 1.58: 6888 1.58 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14820 Sorted by residual: bond pdb=" BE BEF B 403 " pdb=" F2 BEF B 403 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" BE BEF A 403 " pdb=" F2 BEF A 403 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" BE BEF E 403 " pdb=" F2 BEF E 403 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" BE BEF D 403 " pdb=" F2 BEF D 403 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" BE BEF C 403 " pdb=" F2 BEF C 403 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 14815 not shown) Histogram of bond angle deviations from ideal: 100.11 - 107.33: 675 107.33 - 114.55: 8639 114.55 - 121.76: 7557 121.76 - 128.98: 3139 128.98 - 136.20: 95 Bond angle restraints: 20105 Sorted by residual: angle pdb=" F2 BEF A 403 " pdb=" BE BEF A 403 " pdb=" F3 BEF A 403 " ideal model delta sigma weight residual 119.96 106.63 13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" F2 BEF E 403 " pdb=" BE BEF E 403 " pdb=" F3 BEF E 403 " ideal model delta sigma weight residual 119.96 106.63 13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" F2 BEF B 403 " pdb=" BE BEF B 403 " pdb=" F3 BEF B 403 " ideal model delta sigma weight residual 119.96 106.64 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" F2 BEF C 403 " pdb=" BE BEF C 403 " pdb=" F3 BEF C 403 " ideal model delta sigma weight residual 119.96 106.64 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" F2 BEF D 403 " pdb=" BE BEF D 403 " pdb=" F3 BEF D 403 " ideal model delta sigma weight residual 119.96 106.67 13.29 3.00e+00 1.11e-01 1.96e+01 ... (remaining 20100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.33: 8735 30.33 - 60.66: 140 60.66 - 91.00: 25 91.00 - 121.33: 0 121.33 - 151.66: 10 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.66 -151.66 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.64 -151.64 1 2.00e+01 2.50e-03 4.51e+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 -60.00 91.63 -151.63 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1122 0.028 - 0.055: 720 0.055 - 0.083: 224 0.083 - 0.111: 112 0.111 - 0.138: 52 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CA ILE B 136 " pdb=" N ILE B 136 " pdb=" C ILE B 136 " pdb=" CB ILE B 136 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE C 136 " pdb=" N ILE C 136 " pdb=" C ILE C 136 " pdb=" CB ILE C 136 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 136 " pdb=" N ILE A 136 " pdb=" C ILE A 136 " pdb=" CB ILE A 136 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO D 243 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.15e+00 pdb=" N PRO C 243 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO A 243 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.015 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 622 2.72 - 3.26: 15419 3.26 - 3.81: 27444 3.81 - 4.35: 36138 4.35 - 4.90: 56968 Nonbonded interactions: 136591 Sorted by model distance: nonbonded pdb="CA CA D 402 " pdb=" F2 BEF D 403 " model vdw 2.173 2.460 nonbonded pdb="CA CA A 402 " pdb=" F2 BEF A 403 " model vdw 2.173 2.460 nonbonded pdb="CA CA C 402 " pdb=" F2 BEF C 403 " model vdw 2.174 2.460 nonbonded pdb="CA CA E 402 " pdb=" F2 BEF E 403 " model vdw 2.174 2.460 nonbonded pdb="CA CA B 402 " pdb=" F2 BEF B 403 " model vdw 2.174 2.460 ... (remaining 136586 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: 5.750 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: 12.920 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 42.760 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 14820 Z= 0.283 Angle : 0.628 13.330 20105 Z= 0.287 Chirality : 0.043 0.138 2230 Planarity : 0.004 0.027 2565 Dihedral : 13.272 151.658 5510 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.65 % Allowed : 3.23 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 1795 helix: -2.30 (0.14), residues: 785 sheet: -0.32 (0.26), residues: 330 loop : 0.94 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 340 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 262 TYR 0.008 0.001 TYR B 143 ARG 0.003 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 267 time to evaluate : 1.689 Fit side-chains REVERT: C 286 ASP cc_start: 0.7473 (m-30) cc_final: 0.7225 (m-30) REVERT: A 325 MET cc_start: 0.8792 (mmp) cc_final: 0.8531 (mmp) REVERT: B 118 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8311 (tmtt) REVERT: B 227 MET cc_start: 0.9102 (mmm) cc_final: 0.8852 (mmm) REVERT: D 128 ASN cc_start: 0.8190 (m110) cc_final: 0.7964 (m-40) outliers start: 10 outliers final: 0 residues processed: 276 average time/residue: 1.5895 time to fit residues: 473.8939 Evaluate side-chains 197 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN A 59 GLN A 225 ASN A 263 GLN A 354 GLN B 246 GLN B 353 GLN D 59 GLN E 353 GLN E 360 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14820 Z= 0.293 Angle : 0.639 8.005 20105 Z= 0.312 Chirality : 0.047 0.160 2230 Planarity : 0.005 0.038 2565 Dihedral : 12.753 158.365 2059 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.58 % Allowed : 8.06 % Favored : 89.35 % 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: 0.10 (0.20), residues: 1795 helix: -0.81 (0.16), residues: 795 sheet: -0.15 (0.28), residues: 300 loop : 1.69 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.006 0.001 HIS A 161 PHE 0.014 0.002 PHE D 262 TYR 0.011 0.001 TYR E 143 ARG 0.005 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 2.262 Fit side-chains REVERT: C 118 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8371 (tttm) REVERT: C 286 ASP cc_start: 0.7489 (m-30) cc_final: 0.7191 (m-30) REVERT: C 314 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: A 118 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7798 (tmtt) REVERT: B 118 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8224 (tmtt) REVERT: B 176 MET cc_start: 0.8007 (mmt) cc_final: 0.7762 (tpp) REVERT: B 227 MET cc_start: 0.9117 (mmm) cc_final: 0.8888 (mmm) REVERT: E 82 MET cc_start: 0.8814 (tpt) cc_final: 0.8514 (tpt) outliers start: 40 outliers final: 8 residues processed: 224 average time/residue: 1.5211 time to fit residues: 370.6181 Evaluate side-chains 204 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 59 GLN A 225 ASN A 263 GLN B 246 GLN B 353 GLN D 59 GLN E 40 HIS E 225 ASN E 353 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14820 Z= 0.235 Angle : 0.599 7.737 20105 Z= 0.288 Chirality : 0.046 0.152 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.650 160.387 2059 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.00 % Allowed : 9.48 % Favored : 88.52 % 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: 0.62 (0.20), residues: 1795 helix: -0.26 (0.18), residues: 795 sheet: 0.04 (0.26), residues: 330 loop : 1.93 (0.27), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 340 HIS 0.005 0.001 HIS A 161 PHE 0.012 0.002 PHE B 262 TYR 0.008 0.001 TYR E 143 ARG 0.006 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.618 Fit side-chains REVERT: C 118 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8346 (tttm) REVERT: C 119 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7594 (ttm) REVERT: C 286 ASP cc_start: 0.7477 (m-30) cc_final: 0.7204 (m-30) REVERT: C 314 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: A 118 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7773 (tmtt) REVERT: A 121 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: B 118 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8336 (tptm) REVERT: B 176 MET cc_start: 0.7989 (mmt) cc_final: 0.7782 (tpp) REVERT: D 355 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6943 (mtp) REVERT: E 82 MET cc_start: 0.8798 (tpt) cc_final: 0.8552 (tpt) outliers start: 31 outliers final: 6 residues processed: 217 average time/residue: 1.5207 time to fit residues: 357.5163 Evaluate side-chains 208 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 297 ASN A 59 GLN A 225 ASN A 263 GLN B 246 GLN E 225 ASN E 353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14820 Z= 0.169 Angle : 0.558 7.329 20105 Z= 0.265 Chirality : 0.044 0.146 2230 Planarity : 0.003 0.033 2565 Dihedral : 12.510 160.399 2059 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.81 % Allowed : 10.39 % Favored : 87.81 % 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: 0.87 (0.20), residues: 1795 helix: 0.00 (0.18), residues: 795 sheet: 0.12 (0.27), residues: 330 loop : 2.01 (0.27), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE B 262 TYR 0.008 0.001 TYR D 69 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 1.459 Fit side-chains REVERT: C 119 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7647 (ttm) REVERT: C 286 ASP cc_start: 0.7443 (m-30) cc_final: 0.7174 (m-30) REVERT: C 314 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: A 100 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: B 118 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8334 (tptm) REVERT: B 176 MET cc_start: 0.7963 (mmt) cc_final: 0.7705 (tpp) REVERT: D 355 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6923 (mtp) outliers start: 28 outliers final: 4 residues processed: 221 average time/residue: 1.5230 time to fit residues: 366.8828 Evaluate side-chains 208 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 355 MET 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: 5.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN C 353 GLN A 225 ASN A 263 GLN B 246 GLN B 353 GLN E 225 ASN E 353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 14820 Z= 0.558 Angle : 0.776 9.675 20105 Z= 0.386 Chirality : 0.056 0.233 2230 Planarity : 0.006 0.052 2565 Dihedral : 13.064 163.344 2059 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.94 % Allowed : 9.87 % Favored : 88.19 % 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: 0.65 (0.20), residues: 1795 helix: -0.15 (0.18), residues: 795 sheet: -0.10 (0.28), residues: 300 loop : 1.82 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP C 340 HIS 0.010 0.002 HIS C 161 PHE 0.022 0.003 PHE B 262 TYR 0.011 0.002 TYR D 166 ARG 0.007 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 1.893 Fit side-chains REVERT: C 118 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7585 (tmtt) REVERT: C 119 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7582 (ttm) REVERT: C 286 ASP cc_start: 0.7548 (m-30) cc_final: 0.7254 (m-30) REVERT: A 100 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: A 118 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7814 (tmtt) REVERT: A 176 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7427 (mmt) REVERT: B 176 MET cc_start: 0.8001 (mmt) cc_final: 0.7786 (tpp) REVERT: B 227 MET cc_start: 0.9101 (mmm) cc_final: 0.8873 (mmm) outliers start: 30 outliers final: 9 residues processed: 209 average time/residue: 1.5413 time to fit residues: 349.7481 Evaluate side-chains 201 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 288 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 263 GLN E 353 GLN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14820 Z= 0.236 Angle : 0.609 7.885 20105 Z= 0.293 Chirality : 0.046 0.159 2230 Planarity : 0.004 0.036 2565 Dihedral : 12.741 159.820 2059 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.87 % Allowed : 10.52 % Favored : 87.61 % 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 (0.20), residues: 1795 helix: 0.02 (0.18), residues: 795 sheet: -0.09 (0.28), residues: 300 loop : 1.89 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.005 0.001 HIS A 161 PHE 0.013 0.002 PHE B 262 TYR 0.008 0.001 TYR D 69 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 1.682 Fit side-chains REVERT: C 118 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8385 (tttm) REVERT: C 119 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7581 (ttm) REVERT: C 121 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: C 286 ASP cc_start: 0.7483 (m-30) cc_final: 0.7211 (m-30) REVERT: C 314 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: B 100 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: B 118 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7147 (tmtp) REVERT: B 227 MET cc_start: 0.9115 (mmm) cc_final: 0.8834 (mmm) REVERT: D 355 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6932 (mtp) outliers start: 29 outliers final: 8 residues processed: 210 average time/residue: 1.4948 time to fit residues: 340.4345 Evaluate side-chains 210 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 225 ASN A 263 GLN B 353 GLN E 353 GLN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14820 Z= 0.144 Angle : 0.547 7.016 20105 Z= 0.258 Chirality : 0.043 0.145 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.474 161.265 2059 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.16 % Allowed : 11.48 % Favored : 87.35 % 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: 1.03 (0.21), residues: 1795 helix: 0.21 (0.18), residues: 795 sheet: 0.13 (0.27), residues: 330 loop : 2.02 (0.27), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE B 255 TYR 0.009 0.001 TYR D 69 ARG 0.007 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 1.819 Fit side-chains REVERT: C 118 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8436 (tttm) REVERT: C 119 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7635 (ttm) REVERT: C 121 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: C 286 ASP cc_start: 0.7404 (m-30) cc_final: 0.7167 (m-30) REVERT: C 314 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: A 100 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: B 118 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8199 (tmtt) REVERT: B 176 MET cc_start: 0.7984 (mmt) cc_final: 0.7713 (tpp) REVERT: B 227 MET cc_start: 0.9130 (mmm) cc_final: 0.8794 (mmm) REVERT: D 226 GLU cc_start: 0.8261 (tp30) cc_final: 0.8025 (tp30) REVERT: D 355 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6922 (mtp) outliers start: 18 outliers final: 3 residues processed: 214 average time/residue: 1.5178 time to fit residues: 353.0372 Evaluate side-chains 204 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 263 GLN E 225 ASN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14820 Z= 0.361 Angle : 0.670 8.609 20105 Z= 0.327 Chirality : 0.050 0.183 2230 Planarity : 0.005 0.039 2565 Dihedral : 12.854 163.761 2059 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.29 % Allowed : 11.23 % Favored : 87.48 % 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: 0.88 (0.20), residues: 1795 helix: 0.08 (0.18), residues: 795 sheet: -0.05 (0.29), residues: 300 loop : 1.91 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 340 HIS 0.007 0.002 HIS E 88 PHE 0.016 0.002 PHE B 262 TYR 0.009 0.001 TYR D 166 ARG 0.007 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.674 Fit side-chains REVERT: C 118 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7512 (tmtt) REVERT: C 119 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7587 (ttm) REVERT: C 121 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: C 286 ASP cc_start: 0.7496 (m-30) cc_final: 0.7217 (m-30) REVERT: C 314 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: A 100 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: B 100 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: B 118 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7151 (tmtp) REVERT: D 355 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6937 (mtp) outliers start: 20 outliers final: 8 residues processed: 202 average time/residue: 1.5491 time to fit residues: 339.5417 Evaluate side-chains 201 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 355 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 0.0070 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 263 GLN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14820 Z= 0.156 Angle : 0.558 7.209 20105 Z= 0.265 Chirality : 0.044 0.145 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.520 161.799 2059 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.03 % Allowed : 11.74 % Favored : 87.23 % 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: 1.06 (0.21), residues: 1795 helix: 0.23 (0.18), residues: 795 sheet: 0.17 (0.27), residues: 330 loop : 2.02 (0.27), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE B 262 TYR 0.009 0.001 TYR D 69 ARG 0.007 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 1.862 Fit side-chains REVERT: C 118 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8437 (tttm) REVERT: C 119 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7619 (ttm) REVERT: C 121 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: C 286 ASP cc_start: 0.7412 (m-30) cc_final: 0.7176 (m-30) REVERT: C 314 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: B 118 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8186 (tmtt) REVERT: B 227 MET cc_start: 0.9075 (mmm) cc_final: 0.8723 (mmm) REVERT: D 355 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6911 (mtp) outliers start: 16 outliers final: 5 residues processed: 206 average time/residue: 1.5410 time to fit residues: 344.7276 Evaluate side-chains 206 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.0770 chunk 104 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 225 ASN A 263 GLN B 353 GLN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14820 Z= 0.211 Angle : 0.588 7.535 20105 Z= 0.281 Chirality : 0.045 0.149 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.599 163.656 2059 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.77 % Allowed : 12.19 % Favored : 87.03 % 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: 1.06 (0.20), residues: 1795 helix: 0.25 (0.18), residues: 790 sheet: 0.19 (0.27), residues: 330 loop : 1.97 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.005 0.001 HIS A 161 PHE 0.011 0.001 PHE B 262 TYR 0.008 0.001 TYR D 69 ARG 0.008 0.000 ARG D 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 1.530 Fit side-chains REVERT: C 118 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8365 (tttm) REVERT: C 119 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7614 (ttm) REVERT: C 121 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: C 286 ASP cc_start: 0.7438 (m-30) cc_final: 0.7182 (m-30) REVERT: C 314 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: D 355 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6921 (mtp) outliers start: 12 outliers final: 5 residues processed: 197 average time/residue: 1.5990 time to fit residues: 341.4057 Evaluate side-chains 198 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 263 GLN ** E 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104072 restraints weight = 13838.220| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.10 r_work: 0.3041 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14820 Z= 0.307 Angle : 0.644 8.113 20105 Z= 0.312 Chirality : 0.048 0.167 2230 Planarity : 0.004 0.050 2565 Dihedral : 12.747 163.319 2055 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.03 % Allowed : 11.87 % Favored : 87.10 % 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: 0.93 (0.20), residues: 1795 helix: 0.16 (0.18), residues: 790 sheet: -0.01 (0.29), residues: 300 loop : 1.87 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 340 HIS 0.006 0.001 HIS A 161 PHE 0.015 0.002 PHE B 262 TYR 0.007 0.001 TYR D 166 ARG 0.009 0.001 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6535.94 seconds wall clock time: 115 minutes 40.94 seconds (6940.94 seconds total)