Starting phenix.real_space_refine on Sat Mar 16 12:51:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/03_2024/7q8b_13863_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/03_2024/7q8b_13863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/03_2024/7q8b_13863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/03_2024/7q8b_13863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/03_2024/7q8b_13863_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/03_2024/7q8b_13863_updated.pdb" } resolution = 3.3 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= 1.000 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 115 5.16 5 C 9195 2.51 5 N 2470 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 14640 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "B" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "D" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "E" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} 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: "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: "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} Time building chain proxies: 8.01, per 1000 atoms: 0.55 Number of scatterers: 14640 At special positions: 0 Unit cell: (79.54, 98.94, 194, 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 115 16.00 P 15 15.00 Mg 5 11.99 O 2840 8.00 N 2470 7.00 C 9195 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.70 Conformation dependent library (CDL) restraints added in 2.9 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 25 sheets defined 44.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... 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 195 removed outlier: 4.052A pdb=" N MET A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.626A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.720A pdb=" N ARG A 255 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS A 256 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.605A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 294 " --> pdb=" O ARG A 291 " (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 removed outlier: 3.538A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.961A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.682A pdb=" N THR A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 370 through 373 No H-bonds generated for 'chain 'A' and resid 370 through 373' 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 195 removed outlier: 4.052A pdb=" N MET B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.626A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.720A pdb=" N ARG B 255 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS B 256 " --> pdb=" O ARG B 253 " (cutoff:3.500A) Proline residue: B 257 - end of helix Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.605A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 294 " --> pdb=" O ARG B 291 " (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 removed outlier: 3.538A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.961A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.682A pdb=" N THR B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 370 through 373 No H-bonds generated for 'chain 'B' and resid 370 through 373' 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 195 removed outlier: 4.052A pdb=" N MET C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.626A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.720A pdb=" N ARG C 255 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS C 256 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Proline residue: C 257 - end of helix Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.604A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 294 " --> pdb=" O ARG C 291 " (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 removed outlier: 3.538A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.962A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.682A pdb=" N THR C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 370 through 373 No H-bonds generated for 'chain 'C' and resid 370 through 373' 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 195 removed outlier: 4.052A pdb=" N MET D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.627A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 251 through 260 removed outlier: 3.720A pdb=" N ARG D 255 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS D 256 " --> pdb=" O ARG D 253 " (cutoff:3.500A) Proline residue: D 257 - end of helix Processing helix chain 'D' and resid 263 through 266 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.605A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 294 " --> pdb=" O ARG D 291 " (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 removed outlier: 3.538A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 4.962A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.681A pdb=" N THR D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 370 through 373 No H-bonds generated for 'chain 'D' and resid 370 through 373' 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 195 removed outlier: 4.052A pdb=" N MET E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.625A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 233 Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.720A pdb=" N ARG E 255 " --> pdb=" O GLN E 252 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS E 256 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Proline residue: E 257 - end of helix Processing helix chain 'E' and resid 263 through 266 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.604A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR E 294 " --> pdb=" O ARG E 291 " (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 removed outlier: 3.539A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 348 removed outlier: 4.962A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.683A pdb=" N THR E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 370 through 373 No H-bonds generated for 'chain 'E' and resid 370 through 373' Processing sheet with id= A, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.173A pdb=" N ASN A 102 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS A 10 " --> pdb=" O ASN A 102 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A 104 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 16 through 19 Processing sheet with id= C, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= F, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.173A pdb=" N ASN B 102 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N CYS B 10 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 16 through 19 Processing sheet with id= H, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= I, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= K, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.173A pdb=" N ASN C 102 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N CYS C 10 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU C 104 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 16 through 19 Processing sheet with id= M, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= N, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= P, first strand: chain 'D' and resid 7 through 10 removed outlier: 6.173A pdb=" N ASN D 102 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N CYS D 10 " --> pdb=" O ASN D 102 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 16 through 19 Processing sheet with id= R, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= U, first strand: chain 'E' and resid 7 through 10 removed outlier: 6.174A pdb=" N ASN E 102 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N CYS E 10 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU E 104 " --> pdb=" O CYS E 10 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 16 through 19 Processing sheet with id= W, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= X, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.407A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 237 through 240 510 hydrogen bonds defined for protein. 1245 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: 4.35 Time building geometry restraints manager: 6.22 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: 4765 1.34 - 1.46: 2258 1.46 - 1.57: 7712 1.57 - 1.69: 15 1.69 - 1.81: 205 Bond restraints: 14955 Sorted by residual: bond pdb=" O3 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" O3 PO4 E 803 " pdb=" P PO4 E 803 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" O3 PO4 C 803 " pdb=" P PO4 C 803 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" O3 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" O3 PO4 D 803 " pdb=" P PO4 D 803 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.60e+00 ... (remaining 14950 not shown) Histogram of bond angle deviations from ideal: 99.96 - 107.19: 669 107.19 - 114.42: 8726 114.42 - 121.65: 7556 121.65 - 128.88: 3224 128.88 - 136.11: 105 Bond angle restraints: 20280 Sorted by residual: angle pdb=" O1B ADP B 802 " pdb=" PB ADP B 802 " pdb=" O3B ADP B 802 " ideal model delta sigma weight residual 119.90 114.06 5.84 3.00e+00 1.11e-01 3.79e+00 angle pdb=" O1B ADP D 802 " pdb=" PB ADP D 802 " pdb=" O3B ADP D 802 " ideal model delta sigma weight residual 119.90 114.07 5.83 3.00e+00 1.11e-01 3.77e+00 angle pdb=" O1B ADP C 802 " pdb=" PB ADP C 802 " pdb=" O3B ADP C 802 " ideal model delta sigma weight residual 119.90 114.10 5.80 3.00e+00 1.11e-01 3.74e+00 angle pdb=" O1B ADP A 802 " pdb=" PB ADP A 802 " pdb=" O3B ADP A 802 " ideal model delta sigma weight residual 119.90 114.11 5.79 3.00e+00 1.11e-01 3.73e+00 angle pdb=" O1B ADP E 802 " pdb=" PB ADP E 802 " pdb=" O3B ADP E 802 " ideal model delta sigma weight residual 119.90 114.12 5.78 3.00e+00 1.11e-01 3.72e+00 ... (remaining 20275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.11: 8940 29.11 - 58.22: 85 58.22 - 87.32: 0 87.32 - 116.43: 5 116.43 - 145.54: 10 Dihedral angle restraints: 9040 sinusoidal: 3700 harmonic: 5340 Sorted by residual: dihedral pdb=" C5' ADP E 802 " pdb=" O5' ADP E 802 " pdb=" PA ADP E 802 " pdb=" O2A ADP E 802 " ideal model delta sinusoidal sigma weight residual 300.00 154.46 145.54 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP C 802 " pdb=" O5' ADP C 802 " pdb=" PA ADP C 802 " pdb=" O2A ADP C 802 " ideal model delta sinusoidal sigma weight residual 300.00 154.49 145.52 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual 300.00 154.49 145.52 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 9037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1073 0.024 - 0.048: 585 0.048 - 0.073: 287 0.073 - 0.097: 127 0.097 - 0.121: 163 Chirality restraints: 2235 Sorted by residual: chirality pdb=" CA ILE C 297 " pdb=" N ILE C 297 " pdb=" C ILE C 297 " pdb=" CB ILE C 297 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE B 297 " pdb=" N ILE B 297 " pdb=" C ILE B 297 " pdb=" CB ILE B 297 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 2232 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 90 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C PHE E 90 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE E 90 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR E 91 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 90 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C PHE B 90 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE B 90 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR B 91 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 90 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C PHE A 90 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE A 90 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 91 " 0.009 2.00e-02 2.50e+03 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 129 2.59 - 3.17: 12239 3.17 - 3.74: 22543 3.74 - 4.32: 33678 4.32 - 4.90: 55827 Nonbonded interactions: 124416 Sorted by model distance: nonbonded pdb="MG MG C 801 " pdb=" O2B ADP C 802 " model vdw 2.012 2.170 nonbonded pdb="MG MG B 801 " pdb=" O2B ADP B 802 " model vdw 2.012 2.170 nonbonded pdb="MG MG A 801 " pdb=" O2B ADP A 802 " model vdw 2.012 2.170 nonbonded pdb="MG MG E 801 " pdb=" O2B ADP E 802 " model vdw 2.012 2.170 nonbonded pdb="MG MG D 801 " pdb=" O2B ADP D 802 " model vdw 2.012 2.170 ... (remaining 124411 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: 0.950 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: 4.180 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 40.990 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 0.063 14955 Z= 0.245 Angle : 0.502 5.840 20280 Z= 0.234 Chirality : 0.046 0.121 2235 Planarity : 0.004 0.027 2605 Dihedral : 10.849 145.539 5610 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: 1.33 (0.20), residues: 1840 helix: 0.78 (0.20), residues: 730 sheet: 0.20 (0.28), residues: 330 loop : 1.63 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 79 HIS 0.003 0.001 HIS C 173 PHE 0.007 0.001 PHE D 254 TYR 0.011 0.001 TYR B 143 ARG 0.002 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.694 Fit side-chains REVERT: A 305 MET cc_start: 0.8172 (tpp) cc_final: 0.7955 (mmt) REVERT: B 355 MET cc_start: 0.7734 (mtp) cc_final: 0.7444 (mtp) REVERT: C 42 GLN cc_start: 0.7819 (tt0) cc_final: 0.7566 (tt0) REVERT: E 82 MET cc_start: 0.8937 (tpt) cc_final: 0.8728 (tpt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3035 time to fit residues: 103.6408 Evaluate side-chains 166 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 235 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14955 Z= 0.364 Angle : 0.633 7.462 20280 Z= 0.307 Chirality : 0.051 0.137 2235 Planarity : 0.005 0.035 2605 Dihedral : 10.796 129.138 2045 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.23 % Allowed : 5.99 % Favored : 92.78 % 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 (0.20), residues: 1840 helix: 0.26 (0.20), residues: 730 sheet: 0.12 (0.27), residues: 340 loop : 1.33 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 79 HIS 0.006 0.001 HIS B 173 PHE 0.015 0.002 PHE C 223 TYR 0.015 0.002 TYR E 294 ARG 0.004 0.001 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: C 42 GLN cc_start: 0.7839 (tt0) cc_final: 0.7581 (tt0) REVERT: C 355 MET cc_start: 0.7843 (mtp) cc_final: 0.7619 (mtp) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 0.2953 time to fit residues: 74.1550 Evaluate side-chains 161 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 235 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14955 Z= 0.425 Angle : 0.632 6.722 20280 Z= 0.306 Chirality : 0.052 0.150 2235 Planarity : 0.005 0.039 2605 Dihedral : 10.989 151.048 2045 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.42 % Allowed : 7.78 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1840 helix: 0.15 (0.20), residues: 725 sheet: -0.11 (0.27), residues: 330 loop : 0.93 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 79 HIS 0.005 0.001 HIS A 161 PHE 0.014 0.002 PHE E 254 TYR 0.012 0.002 TYR D 294 ARG 0.004 0.001 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: C 42 GLN cc_start: 0.7768 (tt0) cc_final: 0.7493 (tt0) REVERT: D 248 MET cc_start: 0.8193 (mmm) cc_final: 0.7970 (mmt) outliers start: 23 outliers final: 17 residues processed: 168 average time/residue: 0.2768 time to fit residues: 68.3809 Evaluate side-chains 163 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14955 Z= 0.326 Angle : 0.587 6.561 20280 Z= 0.281 Chirality : 0.049 0.137 2235 Planarity : 0.004 0.041 2605 Dihedral : 10.898 155.520 2045 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.42 % Allowed : 9.51 % Favored : 89.07 % 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: 0.46 (0.20), residues: 1840 helix: 0.15 (0.20), residues: 720 sheet: -0.05 (0.27), residues: 330 loop : 0.92 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS B 161 PHE 0.013 0.001 PHE C 254 TYR 0.011 0.001 TYR D 69 ARG 0.004 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 353 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8124 (mm110) REVERT: C 42 GLN cc_start: 0.7731 (tt0) cc_final: 0.7495 (tt0) REVERT: D 248 MET cc_start: 0.8174 (mmm) cc_final: 0.7934 (mmt) outliers start: 23 outliers final: 20 residues processed: 165 average time/residue: 0.2796 time to fit residues: 68.2113 Evaluate side-chains 157 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 123 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 100 GLN C 235 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14955 Z= 0.141 Angle : 0.517 6.414 20280 Z= 0.241 Chirality : 0.046 0.129 2235 Planarity : 0.004 0.041 2605 Dihedral : 10.572 159.347 2045 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.93 % Allowed : 11.17 % Favored : 87.90 % 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: 0.78 (0.20), residues: 1840 helix: 0.35 (0.20), residues: 720 sheet: 0.14 (0.27), residues: 330 loop : 1.15 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE D 254 TYR 0.008 0.001 TYR C 143 ARG 0.001 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.692 Fit side-chains revert: symmetry clash REVERT: C 42 GLN cc_start: 0.7674 (tt0) cc_final: 0.7461 (tt0) REVERT: D 248 MET cc_start: 0.8161 (mmm) cc_final: 0.7881 (mmt) outliers start: 15 outliers final: 8 residues processed: 163 average time/residue: 0.2695 time to fit residues: 64.9699 Evaluate side-chains 154 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.1980 chunk 161 optimal weight: 10.0000 chunk 35 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 215 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14955 Z= 0.210 Angle : 0.535 6.639 20280 Z= 0.250 Chirality : 0.047 0.124 2235 Planarity : 0.004 0.042 2605 Dihedral : 10.613 159.799 2045 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.05 % Allowed : 11.60 % 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: 0.82 (0.20), residues: 1840 helix: 0.36 (0.20), residues: 725 sheet: 0.19 (0.27), residues: 330 loop : 1.20 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS A 161 PHE 0.011 0.001 PHE E 254 TYR 0.009 0.001 TYR E 143 ARG 0.002 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.816 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 159 average time/residue: 0.2782 time to fit residues: 64.8316 Evaluate side-chains 157 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN C 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14955 Z= 0.307 Angle : 0.569 6.665 20280 Z= 0.269 Chirality : 0.049 0.132 2235 Planarity : 0.004 0.041 2605 Dihedral : 10.823 163.417 2045 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 12.04 % Favored : 86.85 % 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: 0.68 (0.20), residues: 1840 helix: 0.30 (0.20), residues: 720 sheet: 0.14 (0.27), residues: 330 loop : 1.03 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS D 161 PHE 0.012 0.001 PHE C 254 TYR 0.009 0.001 TYR C 143 ARG 0.002 0.000 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: D 248 MET cc_start: 0.8143 (mmm) cc_final: 0.7873 (mmt) outliers start: 18 outliers final: 16 residues processed: 163 average time/residue: 0.2750 time to fit residues: 66.6245 Evaluate side-chains 158 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 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 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14955 Z= 0.270 Angle : 0.559 6.643 20280 Z= 0.263 Chirality : 0.048 0.140 2235 Planarity : 0.004 0.040 2605 Dihedral : 10.853 166.315 2045 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.17 % Allowed : 12.22 % Favored : 86.60 % 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: 0.39 (0.20), residues: 1840 helix: 0.07 (0.19), residues: 750 sheet: 0.15 (0.27), residues: 330 loop : 0.81 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.012 0.001 PHE E 254 TYR 0.009 0.001 TYR D 69 ARG 0.002 0.000 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.743 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 18 residues processed: 160 average time/residue: 0.2685 time to fit residues: 63.7248 Evaluate side-chains 161 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 165 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14955 Z= 0.144 Angle : 0.512 6.504 20280 Z= 0.236 Chirality : 0.046 0.127 2235 Planarity : 0.004 0.042 2605 Dihedral : 10.674 177.927 2045 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.86 % Allowed : 12.65 % Favored : 86.48 % 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: 0.67 (0.20), residues: 1840 helix: 0.27 (0.19), residues: 750 sheet: 0.32 (0.27), residues: 330 loop : 0.99 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE D 254 TYR 0.007 0.001 TYR B 143 ARG 0.001 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.688 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 158 average time/residue: 0.2625 time to fit residues: 61.8682 Evaluate side-chains 156 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 0.0980 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 89 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14955 Z= 0.153 Angle : 0.513 6.571 20280 Z= 0.236 Chirality : 0.046 0.132 2235 Planarity : 0.004 0.042 2605 Dihedral : 10.472 173.305 2045 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.74 % Allowed : 13.15 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1840 helix: 0.36 (0.19), residues: 750 sheet: 0.43 (0.27), residues: 330 loop : 1.05 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE D 254 TYR 0.008 0.001 TYR E 143 ARG 0.001 0.000 ARG B 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.750 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 155 average time/residue: 0.2612 time to fit residues: 60.4724 Evaluate side-chains 156 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.090106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.078437 restraints weight = 23090.888| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.10 r_work: 0.2750 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14955 Z= 0.208 Angle : 0.529 6.619 20280 Z= 0.245 Chirality : 0.047 0.138 2235 Planarity : 0.004 0.042 2605 Dihedral : 10.427 173.406 2045 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.74 % Allowed : 13.21 % 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: 0.74 (0.20), residues: 1840 helix: 0.34 (0.19), residues: 750 sheet: 0.40 (0.27), residues: 330 loop : 0.99 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS B 161 PHE 0.011 0.001 PHE E 254 TYR 0.009 0.001 TYR E 143 ARG 0.002 0.000 ARG E 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2681.87 seconds wall clock time: 49 minutes 33.99 seconds (2973.99 seconds total)