Starting phenix.real_space_refine on Sun Feb 18 05:35:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/02_2024/8dtp_27707_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/02_2024/8dtp_27707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/02_2024/8dtp_27707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/02_2024/8dtp_27707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/02_2024/8dtp_27707_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/02_2024/8dtp_27707_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 27 5.49 5 Mg 5 5.21 5 S 119 5.16 5 C 13244 2.51 5 N 3469 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 82": "OD1" <-> "OD2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.69, per 1000 atoms: 0.56 Number of scatterers: 20944 At special positions: 0 Unit cell: (112.608, 134.136, 141.588, 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 119 16.00 P 27 15.00 Mg 5 11.99 O 4080 8.00 N 3469 7.00 C 13244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.22 Conformation dependent library (CDL) restraints added in 3.8 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 12 sheets defined 47.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 22 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 87 through 117 Processing helix chain 'A' and resid 131 through 142 Proline residue: A 135 - end of helix removed outlier: 3.787A pdb=" N MET A 138 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.708A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.728A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 13 through 22 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 89 through 118 Processing helix chain 'B' and resid 131 through 142 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 377 through 380 No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 53 through 62 Processing helix chain 'C' and resid 67 through 76 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 118 Processing helix chain 'C' and resid 131 through 142 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 163 through 166 No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 287 through 300 Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 328 through 346 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.550A pdb=" N ALA C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.609A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Proline residue: D 21 - end of helix Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 53 through 61 Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 87 through 117 Processing helix chain 'D' and resid 131 through 142 Proline residue: D 135 - end of helix removed outlier: 3.522A pdb=" N LEU D 142 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.849A pdb=" N SER D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 328 through 346 Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 376 through 379 No H-bonds generated for 'chain 'D' and resid 376 through 379' Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 13 through 19 removed outlier: 3.593A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 67 through 78 Processing helix chain 'E' and resid 87 through 118 Processing helix chain 'E' and resid 131 through 142 Proline residue: E 135 - end of helix removed outlier: 3.687A pdb=" N GLN E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA E 141 " --> pdb=" O MET E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'E' and resid 247 through 250 No H-bonds generated for 'chain 'E' and resid 247 through 250' Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 328 through 346 removed outlier: 3.843A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 391 through 396 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 14 through 22 Proline residue: F 21 - end of helix Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 53 through 61 Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 89 through 117 Processing helix chain 'F' and resid 131 through 143 Proline residue: F 135 - end of helix removed outlier: 3.870A pdb=" N ALA F 141 " --> pdb=" O MET F 138 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU F 142 " --> pdb=" O ARG F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 203 through 217 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 246 through 251 Processing helix chain 'F' and resid 256 through 268 Processing helix chain 'F' and resid 287 through 301 Processing helix chain 'F' and resid 328 through 346 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing sheet with id= A, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 383 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= C, first strand: chain 'B' and resid 383 through 386 removed outlier: 3.626A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 420 through 422 Processing sheet with id= E, first strand: chain 'C' and resid 402 through 406 removed outlier: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG C 274 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR C 223 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 276 " --> pdb=" O TYR C 223 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER C 225 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS C 278 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 419 through 422 Processing sheet with id= G, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.038A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE D 383 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N MET D 196 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU D 385 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 405 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA D 386 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN D 403 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE D 388 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE D 401 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 220 through 225 removed outlier: 6.316A pdb=" N ARG D 274 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N TYR D 223 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE D 276 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER D 225 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS D 278 " --> pdb=" O SER D 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 416 through 418 removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE E 383 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 194 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG E 274 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N TYR E 223 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE E 276 " --> pdb=" O TYR E 223 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER E 225 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS E 278 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 349 through 352 removed outlier: 6.196A pdb=" N THR F 191 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR F 352 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN F 193 " --> pdb=" O THR F 352 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE F 383 " --> pdb=" O VAL F 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 221 through 225 Processing sheet with id= L, first strand: chain 'F' and resid 419 through 422 861 hydrogen bonds defined for protein. 2454 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: 6.31 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 6695 1.35 - 1.50: 5600 1.50 - 1.65: 8864 1.65 - 1.80: 98 1.80 - 1.95: 111 Bond restraints: 21368 Sorted by residual: bond pdb=" CE1 HIS C 253 " pdb=" NE2 HIS C 253 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.66e+01 bond pdb=" CE1 HIS D 87 " pdb=" NE2 HIS D 87 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.93e+00 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.54: 579 106.54 - 113.48: 11884 113.48 - 120.41: 8188 120.41 - 127.35: 8094 127.35 - 134.28: 221 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-01 1.57e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.08 5.22 1.35e+00 5.49e-01 1.50e+01 angle pdb=" N ASP F 382 " pdb=" CA ASP F 382 " pdb=" C ASP F 382 " ideal model delta sigma weight residual 114.31 109.48 4.83 1.29e+00 6.01e-01 1.40e+01 angle pdb=" N GLU A 122 " pdb=" CA GLU A 122 " pdb=" C GLU A 122 " ideal model delta sigma weight residual 111.71 107.41 4.30 1.15e+00 7.56e-01 1.40e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12753 35.65 - 71.31: 169 71.31 - 106.96: 4 106.96 - 142.61: 1 142.61 - 178.27: 4 Dihedral angle restraints: 12931 sinusoidal: 5317 harmonic: 7614 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.47 -174.20 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.57 157.48 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 12928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2404 0.044 - 0.088: 561 0.088 - 0.132: 237 0.132 - 0.175: 33 0.175 - 0.219: 11 Chirality restraints: 3246 Sorted by residual: chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3243 not shown) Planarity restraints: 3599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C GLU A 373 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C SER B 145 " 0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 122 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C GLU A 122 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU A 122 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 123 " 0.012 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 159 2.56 - 3.14: 16967 3.14 - 3.73: 33544 3.73 - 4.31: 47227 4.31 - 4.90: 78111 Nonbonded interactions: 176008 Sorted by model distance: nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 nonbonded pdb=" OE2 GLU C 227 " pdb="MG MG C 502 " model vdw 2.005 2.170 ... (remaining 176003 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' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } 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: 2.000 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: 0.020 Extract box with map and model: 8.320 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 57.940 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 0.047 21368 Z= 0.276 Angle : 0.633 7.809 28966 Z= 0.424 Chirality : 0.046 0.219 3246 Planarity : 0.004 0.075 3599 Dihedral : 12.189 178.266 8011 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.92 % Allowed : 6.26 % Favored : 91.82 % 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: 0.52 (0.17), residues: 2580 helix: 1.58 (0.15), residues: 1317 sheet: -0.15 (0.30), residues: 345 loop : -1.28 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 351 HIS 0.008 0.001 HIS B 152 PHE 0.023 0.002 PHE D 383 TYR 0.014 0.001 TYR E 329 ARG 0.002 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 549 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8240 (tpt) cc_final: 0.7270 (tpt) REVERT: A 70 TYR cc_start: 0.6704 (t80) cc_final: 0.6445 (t80) REVERT: A 203 LYS cc_start: 0.7948 (mttm) cc_final: 0.7714 (mtmm) REVERT: A 312 TYR cc_start: 0.4815 (t80) cc_final: 0.4605 (t80) REVERT: A 337 GLU cc_start: 0.6337 (mt-10) cc_final: 0.6019 (mt-10) REVERT: B 13 GLN cc_start: 0.7676 (tp40) cc_final: 0.7476 (mp10) REVERT: B 53 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7569 (mm) REVERT: B 57 ASN cc_start: 0.7789 (p0) cc_final: 0.7453 (p0) REVERT: B 71 SER cc_start: 0.8308 (t) cc_final: 0.8103 (m) REVERT: B 96 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7997 (mttm) REVERT: B 109 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7952 (tttt) REVERT: B 330 THR cc_start: 0.7601 (t) cc_final: 0.7358 (m) REVERT: C 92 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7751 (mppt) REVERT: C 177 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7478 (mtm110) REVERT: C 184 LYS cc_start: 0.7702 (mtpp) cc_final: 0.7454 (mtpt) REVERT: C 236 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.7974 (mtp180) REVERT: C 279 GLN cc_start: 0.8193 (tt0) cc_final: 0.7879 (tt0) REVERT: C 313 LEU cc_start: 0.6143 (pp) cc_final: 0.5875 (tt) REVERT: C 317 LYS cc_start: 0.7867 (pttt) cc_final: 0.7623 (pttm) REVERT: D 86 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.5885 (t70) REVERT: D 101 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7935 (mmm160) REVERT: D 153 ASP cc_start: 0.7384 (t0) cc_final: 0.7168 (t70) REVERT: D 177 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7562 (mtm-85) REVERT: D 226 MET cc_start: 0.7580 (mmm) cc_final: 0.7264 (mmm) REVERT: D 227 GLU cc_start: 0.7202 (tt0) cc_final: 0.6784 (pm20) REVERT: D 238 ASP cc_start: 0.8633 (m-30) cc_final: 0.8401 (m-30) REVERT: D 279 GLN cc_start: 0.7722 (tt0) cc_final: 0.6829 (tm130) REVERT: D 331 THR cc_start: 0.7402 (p) cc_final: 0.6992 (m) REVERT: E 92 LYS cc_start: 0.8450 (tppp) cc_final: 0.8158 (ttmt) REVERT: E 109 LYS cc_start: 0.8056 (tptt) cc_final: 0.7715 (tttm) REVERT: E 170 ARG cc_start: 0.6466 (ptt-90) cc_final: 0.6036 (mtp85) REVERT: E 228 MET cc_start: 0.6478 (mmp) cc_final: 0.6160 (mmm) REVERT: E 265 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (mppt) REVERT: E 274 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7708 (mmm-85) REVERT: E 279 GLN cc_start: 0.7177 (pt0) cc_final: 0.6106 (tp40) REVERT: E 384 MET cc_start: 0.6712 (ttm) cc_final: 0.6492 (mtp) REVERT: E 392 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7136 (pm20) REVERT: E 413 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7575 (mttt) REVERT: F 139 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.6925 (ttp-110) REVERT: F 147 ASP cc_start: 0.7469 (m-30) cc_final: 0.7219 (p0) REVERT: F 247 ASP cc_start: 0.7450 (m-30) cc_final: 0.7111 (m-30) REVERT: F 302 ASN cc_start: 0.7693 (t0) cc_final: 0.7382 (t0) REVERT: F 327 ASN cc_start: 0.7051 (p0) cc_final: 0.6696 (p0) REVERT: F 333 LYS cc_start: 0.7406 (ttpp) cc_final: 0.6800 (ttmm) REVERT: F 347 GLU cc_start: 0.7100 (mp0) cc_final: 0.6882 (mm-30) REVERT: F 397 GLU cc_start: 0.6503 (tp30) cc_final: 0.6164 (tm-30) REVERT: F 398 GLN cc_start: 0.7540 (mt0) cc_final: 0.6941 (mp-120) REVERT: F 404 ILE cc_start: 0.8258 (mt) cc_final: 0.7976 (mm) REVERT: F 407 ARG cc_start: 0.6875 (ttp-170) cc_final: 0.6113 (ttm170) outliers start: 43 outliers final: 2 residues processed: 577 average time/residue: 1.4687 time to fit residues: 946.6216 Evaluate side-chains 327 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 322 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 216 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN B 62 ASN C 116 ASN C 302 ASN D 200 ASN E 167 ASN F 62 ASN F 140 GLN F 200 ASN F 295 ASN F 355 GLN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21368 Z= 0.260 Angle : 0.569 8.138 28966 Z= 0.297 Chirality : 0.042 0.221 3246 Planarity : 0.004 0.042 3599 Dihedral : 11.059 177.177 3005 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.20 % Allowed : 13.27 % Favored : 82.53 % 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: 0.37 (0.17), residues: 2580 helix: 1.31 (0.15), residues: 1336 sheet: 0.00 (0.29), residues: 349 loop : -1.26 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 162 HIS 0.005 0.001 HIS A 8 PHE 0.021 0.002 PHE D 65 TYR 0.016 0.002 TYR A 70 ARG 0.005 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 340 time to evaluate : 2.316 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.6938 (t80) cc_final: 0.6656 (t80) REVERT: A 333 LYS cc_start: 0.6437 (ttpt) cc_final: 0.6022 (mmmt) REVERT: A 337 GLU cc_start: 0.6394 (mt-10) cc_final: 0.5733 (mp0) REVERT: B 49 SER cc_start: 0.9120 (t) cc_final: 0.8593 (p) REVERT: B 57 ASN cc_start: 0.7942 (p0) cc_final: 0.7696 (p0) REVERT: B 96 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8039 (mttm) REVERT: B 109 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7910 (tttt) REVERT: B 177 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7667 (mtm110) REVERT: B 298 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8035 (tptt) REVERT: C 92 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7811 (mppt) REVERT: C 101 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8429 (mmm160) REVERT: C 184 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7501 (mtpt) REVERT: C 236 ARG cc_start: 0.8408 (mtt-85) cc_final: 0.8035 (mtp180) REVERT: D 26 GLU cc_start: 0.7405 (mp0) cc_final: 0.7132 (mm-30) REVERT: D 153 ASP cc_start: 0.7577 (t0) cc_final: 0.7235 (t70) REVERT: D 226 MET cc_start: 0.7804 (mmm) cc_final: 0.7422 (mmm) REVERT: D 227 GLU cc_start: 0.7477 (tt0) cc_final: 0.6925 (pm20) REVERT: D 254 ILE cc_start: 0.8103 (tt) cc_final: 0.7898 (pt) REVERT: D 331 THR cc_start: 0.7316 (p) cc_final: 0.6928 (m) REVERT: E 92 LYS cc_start: 0.8518 (tppp) cc_final: 0.8211 (ttmt) REVERT: E 109 LYS cc_start: 0.8137 (tptt) cc_final: 0.7721 (tttm) REVERT: E 124 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6683 (ptm160) REVERT: E 170 ARG cc_start: 0.6513 (ptt-90) cc_final: 0.6081 (mtp85) REVERT: E 196 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7057 (ppp) REVERT: E 279 GLN cc_start: 0.7125 (pt0) cc_final: 0.6067 (tp40) REVERT: E 317 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6718 (ptmt) REVERT: E 413 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7578 (mttt) REVERT: E 427 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8197 (ttmm) REVERT: F 139 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7153 (ttp80) REVERT: F 147 ASP cc_start: 0.7489 (m-30) cc_final: 0.7252 (p0) REVERT: F 302 ASN cc_start: 0.7748 (t0) cc_final: 0.7396 (t0) REVERT: F 327 ASN cc_start: 0.7147 (p0) cc_final: 0.6721 (p0) REVERT: F 333 LYS cc_start: 0.7448 (ttpp) cc_final: 0.6981 (ttmt) REVERT: F 347 GLU cc_start: 0.7209 (mp0) cc_final: 0.6943 (mm-30) REVERT: F 397 GLU cc_start: 0.6683 (tp30) cc_final: 0.6212 (tm-30) REVERT: F 398 GLN cc_start: 0.7474 (mt0) cc_final: 0.6944 (mp-120) REVERT: F 431 ILE cc_start: 0.7049 (pp) cc_final: 0.6608 (pt) outliers start: 94 outliers final: 35 residues processed: 402 average time/residue: 1.3691 time to fit residues: 620.9314 Evaluate side-chains 323 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 285 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 321 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 233 optimal weight: 0.1980 chunk 80 optimal weight: 8.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN C 288 ASN C 302 ASN D 100 GLN D 200 ASN E 57 ASN E 167 ASN F 140 GLN F 200 ASN F 288 ASN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21368 Z= 0.180 Angle : 0.495 6.911 28966 Z= 0.265 Chirality : 0.040 0.176 3246 Planarity : 0.003 0.038 3599 Dihedral : 10.936 179.157 2999 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.93 % Allowed : 14.79 % Favored : 81.28 % 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: 0.49 (0.17), residues: 2580 helix: 1.44 (0.15), residues: 1335 sheet: 0.09 (0.30), residues: 340 loop : -1.28 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.004 0.001 HIS B 8 PHE 0.016 0.002 PHE D 65 TYR 0.010 0.001 TYR F 149 ARG 0.006 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 308 time to evaluate : 2.440 Fit side-chains REVERT: A 1 MET cc_start: 0.8130 (tpt) cc_final: 0.7263 (tpt) REVERT: A 79 LYS cc_start: 0.8324 (ttmp) cc_final: 0.8044 (mtpm) REVERT: A 333 LYS cc_start: 0.6366 (ttpt) cc_final: 0.5996 (mmmt) REVERT: A 337 GLU cc_start: 0.6362 (mt-10) cc_final: 0.5701 (mp0) REVERT: B 57 ASN cc_start: 0.7973 (p0) cc_final: 0.7716 (p0) REVERT: B 96 LYS cc_start: 0.8338 (mtpp) cc_final: 0.7990 (mttt) REVERT: B 109 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7904 (tttt) REVERT: B 177 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7638 (mtm110) REVERT: B 254 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8051 (mm) REVERT: B 270 SER cc_start: 0.7773 (m) cc_final: 0.7542 (p) REVERT: B 355 GLN cc_start: 0.8074 (tp40) cc_final: 0.7828 (tp40) REVERT: C 92 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7807 (mppt) REVERT: C 128 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6655 (mtt) REVERT: C 139 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7477 (mtm110) REVERT: C 313 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6270 (pp) REVERT: D 1 MET cc_start: 0.8465 (ptp) cc_final: 0.8211 (ptm) REVERT: D 26 GLU cc_start: 0.7284 (mp0) cc_final: 0.7012 (mp0) REVERT: D 153 ASP cc_start: 0.7578 (t0) cc_final: 0.7217 (t70) REVERT: D 226 MET cc_start: 0.7843 (mmm) cc_final: 0.7504 (mmm) REVERT: D 227 GLU cc_start: 0.7433 (tt0) cc_final: 0.6919 (pm20) REVERT: D 331 THR cc_start: 0.7331 (p) cc_final: 0.6945 (m) REVERT: D 389 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: E 92 LYS cc_start: 0.8495 (tppp) cc_final: 0.8189 (ttmt) REVERT: E 109 LYS cc_start: 0.8135 (tptt) cc_final: 0.7696 (tttm) REVERT: E 124 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6642 (ptm160) REVERT: E 170 ARG cc_start: 0.6547 (ptt-90) cc_final: 0.6089 (mtp180) REVERT: E 196 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7106 (ppp) REVERT: E 265 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7814 (mppt) REVERT: E 279 GLN cc_start: 0.7133 (pt0) cc_final: 0.6057 (tp40) REVERT: E 389 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: E 413 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7575 (mttt) REVERT: E 427 LYS cc_start: 0.8471 (ttpp) cc_final: 0.8227 (ttmm) REVERT: F 139 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7117 (ttp-110) REVERT: F 147 ASP cc_start: 0.7451 (m-30) cc_final: 0.7219 (p0) REVERT: F 302 ASN cc_start: 0.7780 (t0) cc_final: 0.7415 (t0) REVERT: F 327 ASN cc_start: 0.7059 (p0) cc_final: 0.6620 (p0) REVERT: F 333 LYS cc_start: 0.7310 (ttpp) cc_final: 0.6856 (ttmt) REVERT: F 347 GLU cc_start: 0.7251 (mp0) cc_final: 0.6980 (mm-30) REVERT: F 397 GLU cc_start: 0.6749 (tp30) cc_final: 0.6217 (tm-30) REVERT: F 398 GLN cc_start: 0.7510 (mt0) cc_final: 0.6976 (mp-120) REVERT: F 431 ILE cc_start: 0.7017 (pp) cc_final: 0.6620 (pt) outliers start: 88 outliers final: 34 residues processed: 368 average time/residue: 1.3665 time to fit residues: 567.0831 Evaluate side-chains 326 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 283 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 7.9990 chunk 177 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 236 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 123 optimal weight: 0.0570 chunk 224 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 288 ASN C 167 ASN C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21368 Z= 0.199 Angle : 0.506 7.908 28966 Z= 0.268 Chirality : 0.040 0.157 3246 Planarity : 0.003 0.037 3599 Dihedral : 10.952 177.194 2998 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.20 % Allowed : 15.64 % Favored : 80.16 % 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: 0.47 (0.17), residues: 2580 helix: 1.43 (0.15), residues: 1336 sheet: 0.12 (0.30), residues: 338 loop : -1.30 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 162 HIS 0.004 0.001 HIS A 8 PHE 0.017 0.002 PHE D 65 TYR 0.012 0.001 TYR B 312 ARG 0.006 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 303 time to evaluate : 2.593 Fit side-chains REVERT: A 79 LYS cc_start: 0.8210 (ttmp) cc_final: 0.7925 (mtpm) REVERT: A 333 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.6096 (mmmt) REVERT: A 337 GLU cc_start: 0.6300 (mt-10) cc_final: 0.5795 (mp0) REVERT: A 370 ASP cc_start: 0.6277 (m-30) cc_final: 0.5651 (t70) REVERT: B 57 ASN cc_start: 0.7927 (p0) cc_final: 0.7672 (p0) REVERT: B 96 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8023 (mttt) REVERT: B 109 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7897 (tttt) REVERT: B 177 ARG cc_start: 0.7876 (mtm110) cc_final: 0.7655 (mtm110) REVERT: B 231 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: B 270 SER cc_start: 0.7758 (OUTLIER) cc_final: 0.7540 (p) REVERT: B 274 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.6871 (mtm-85) REVERT: B 355 GLN cc_start: 0.8111 (tp40) cc_final: 0.7817 (tp40) REVERT: B 392 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6312 (mp0) REVERT: C 66 THR cc_start: 0.6366 (OUTLIER) cc_final: 0.6111 (m) REVERT: C 92 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7785 (mppt) REVERT: C 139 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7527 (mtm110) REVERT: C 313 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6338 (pp) REVERT: D 1 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8261 (ptm) REVERT: D 26 GLU cc_start: 0.7352 (mp0) cc_final: 0.7074 (mp0) REVERT: D 139 ARG cc_start: 0.7332 (ttp80) cc_final: 0.6738 (ttp-110) REVERT: D 153 ASP cc_start: 0.7626 (t0) cc_final: 0.7248 (t70) REVERT: D 226 MET cc_start: 0.7911 (mmm) cc_final: 0.7640 (mmm) REVERT: D 227 GLU cc_start: 0.7418 (tt0) cc_final: 0.6910 (pm20) REVERT: D 331 THR cc_start: 0.7236 (p) cc_final: 0.6829 (m) REVERT: D 389 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7722 (tp30) REVERT: E 92 LYS cc_start: 0.8531 (tppp) cc_final: 0.8204 (ttmt) REVERT: E 109 LYS cc_start: 0.8165 (tptt) cc_final: 0.7676 (tttt) REVERT: E 124 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6694 (ptm160) REVERT: E 170 ARG cc_start: 0.6622 (ptt-90) cc_final: 0.6106 (mtp180) REVERT: E 196 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7156 (ppp) REVERT: E 265 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7817 (mppt) REVERT: E 279 GLN cc_start: 0.7116 (pt0) cc_final: 0.6038 (tp40) REVERT: E 317 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6604 (ptmt) REVERT: E 389 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: E 413 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7551 (mttt) REVERT: E 427 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8224 (ttmm) REVERT: F 139 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7148 (ttp-110) REVERT: F 147 ASP cc_start: 0.7448 (m-30) cc_final: 0.7206 (p0) REVERT: F 226 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7740 (mmm) REVERT: F 302 ASN cc_start: 0.7832 (t0) cc_final: 0.7457 (t0) REVERT: F 327 ASN cc_start: 0.7105 (p0) cc_final: 0.6659 (p0) REVERT: F 333 LYS cc_start: 0.7352 (ttpp) cc_final: 0.6890 (ttmt) REVERT: F 347 GLU cc_start: 0.7236 (mp0) cc_final: 0.6974 (mm-30) REVERT: F 397 GLU cc_start: 0.6829 (tp30) cc_final: 0.6228 (tm-30) REVERT: F 398 GLN cc_start: 0.7630 (mt0) cc_final: 0.7059 (mp-120) REVERT: F 431 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6656 (pt) outliers start: 94 outliers final: 43 residues processed: 366 average time/residue: 1.3386 time to fit residues: 554.5317 Evaluate side-chains 341 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 282 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 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 180 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN B 140 GLN C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 21368 Z= 0.427 Angle : 0.672 9.536 28966 Z= 0.350 Chirality : 0.047 0.189 3246 Planarity : 0.004 0.047 3599 Dihedral : 11.510 172.827 2998 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.36 % Allowed : 15.19 % Favored : 79.45 % 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 (0.16), residues: 2580 helix: 0.80 (0.14), residues: 1344 sheet: -0.02 (0.29), residues: 343 loop : -1.36 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 162 HIS 0.007 0.002 HIS E 8 PHE 0.028 0.003 PHE D 65 TYR 0.021 0.002 TYR B 312 ARG 0.004 0.001 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 290 time to evaluate : 2.740 Fit side-chains REVERT: A 79 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7959 (mtpm) REVERT: A 184 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8117 (mmtp) REVERT: A 247 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6661 (p0) REVERT: A 333 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6075 (mmmt) REVERT: A 337 GLU cc_start: 0.6463 (mt-10) cc_final: 0.5968 (mp0) REVERT: A 370 ASP cc_start: 0.6197 (m-30) cc_final: 0.5622 (t70) REVERT: A 411 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7289 (ttmm) REVERT: B 57 ASN cc_start: 0.8205 (p0) cc_final: 0.7977 (p0) REVERT: B 96 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8042 (mttt) REVERT: B 109 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7894 (tttt) REVERT: B 177 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7750 (mtm-85) REVERT: B 231 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: B 270 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7482 (p) REVERT: B 274 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.6930 (mtm-85) REVERT: B 392 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6394 (mp0) REVERT: C 3 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7699 (mt-10) REVERT: C 34 LYS cc_start: 0.7831 (tttt) cc_final: 0.7346 (tptt) REVERT: C 38 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7217 (mtmt) REVERT: C 66 THR cc_start: 0.6356 (OUTLIER) cc_final: 0.6076 (m) REVERT: C 92 LYS cc_start: 0.8214 (mmmm) cc_final: 0.7792 (mppt) REVERT: C 128 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6700 (mtt) REVERT: D 26 GLU cc_start: 0.7420 (mp0) cc_final: 0.7130 (mp0) REVERT: D 153 ASP cc_start: 0.7750 (t0) cc_final: 0.7340 (t70) REVERT: D 226 MET cc_start: 0.7906 (mmm) cc_final: 0.7617 (mmm) REVERT: D 227 GLU cc_start: 0.7628 (tt0) cc_final: 0.7030 (pm20) REVERT: D 243 ASP cc_start: 0.7993 (t0) cc_final: 0.7604 (m-30) REVERT: D 331 THR cc_start: 0.7359 (p) cc_final: 0.7025 (m) REVERT: D 389 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: D 429 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8200 (t) REVERT: E 26 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: E 92 LYS cc_start: 0.8657 (tppp) cc_final: 0.8271 (ttmt) REVERT: E 109 LYS cc_start: 0.8314 (tptt) cc_final: 0.7675 (tttp) REVERT: E 124 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6695 (ptm160) REVERT: E 170 ARG cc_start: 0.6679 (ptt-90) cc_final: 0.6055 (mtp180) REVERT: E 196 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7285 (ppp) REVERT: E 228 MET cc_start: 0.6425 (mmm) cc_final: 0.6016 (ptt) REVERT: E 265 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7745 (mppt) REVERT: E 279 GLN cc_start: 0.7227 (pt0) cc_final: 0.6101 (tp40) REVERT: E 312 TYR cc_start: 0.3669 (t80) cc_final: 0.3334 (t80) REVERT: E 317 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6597 (ptmt) REVERT: E 413 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7596 (mttt) REVERT: E 427 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8244 (ttmm) REVERT: F 139 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7222 (ttp80) REVERT: F 147 ASP cc_start: 0.7582 (m-30) cc_final: 0.7265 (p0) REVERT: F 203 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7645 (mtmm) REVERT: F 228 MET cc_start: 0.8129 (ptm) cc_final: 0.7765 (ptm) REVERT: F 247 ASP cc_start: 0.7518 (m-30) cc_final: 0.7296 (m-30) REVERT: F 302 ASN cc_start: 0.7800 (t0) cc_final: 0.7389 (t0) REVERT: F 327 ASN cc_start: 0.7303 (p0) cc_final: 0.6849 (p0) REVERT: F 333 LYS cc_start: 0.7378 (ttpp) cc_final: 0.6989 (ttmt) REVERT: F 347 GLU cc_start: 0.7257 (mp0) cc_final: 0.6966 (mm-30) REVERT: F 370 ASP cc_start: 0.6187 (m-30) cc_final: 0.5909 (m-30) REVERT: F 397 GLU cc_start: 0.6819 (tp30) cc_final: 0.6146 (tm-30) REVERT: F 398 GLN cc_start: 0.7627 (mt0) cc_final: 0.7036 (mp10) outliers start: 120 outliers final: 50 residues processed: 374 average time/residue: 1.3872 time to fit residues: 584.9746 Evaluate side-chains 345 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 276 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 208 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 140 GLN C 288 ASN C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21368 Z= 0.163 Angle : 0.505 9.477 28966 Z= 0.269 Chirality : 0.040 0.228 3246 Planarity : 0.003 0.033 3599 Dihedral : 11.177 176.168 2998 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.40 % Allowed : 17.61 % Favored : 79.00 % 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: 0.32 (0.17), residues: 2580 helix: 1.27 (0.15), residues: 1331 sheet: 0.06 (0.29), residues: 335 loop : -1.29 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.005 0.001 HIS B 8 PHE 0.012 0.001 PHE D 65 TYR 0.011 0.001 TYR F 158 ARG 0.004 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 291 time to evaluate : 2.631 Fit side-chains REVERT: A 79 LYS cc_start: 0.8219 (ttmp) cc_final: 0.7892 (mtpm) REVERT: A 247 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6615 (p0) REVERT: A 333 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5748 (mmmm) REVERT: A 337 GLU cc_start: 0.6317 (mt-10) cc_final: 0.5763 (mp0) REVERT: A 370 ASP cc_start: 0.6158 (m-30) cc_final: 0.5653 (t70) REVERT: B 46 GLU cc_start: 0.8164 (tt0) cc_final: 0.7964 (mt-10) REVERT: B 57 ASN cc_start: 0.8034 (p0) cc_final: 0.7791 (p0) REVERT: B 96 LYS cc_start: 0.8352 (mtpp) cc_final: 0.7977 (mttt) REVERT: B 231 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: B 270 SER cc_start: 0.7713 (OUTLIER) cc_final: 0.7471 (p) REVERT: B 274 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.6837 (mtm-85) REVERT: B 392 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6327 (mp0) REVERT: C 92 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7808 (mppt) REVERT: C 313 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6434 (pp) REVERT: D 1 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8228 (ptm) REVERT: D 26 GLU cc_start: 0.7429 (mp0) cc_final: 0.7174 (mp0) REVERT: D 139 ARG cc_start: 0.7355 (ttp80) cc_final: 0.6799 (ttp-110) REVERT: D 153 ASP cc_start: 0.7678 (t0) cc_final: 0.7306 (t70) REVERT: D 226 MET cc_start: 0.7891 (mmm) cc_final: 0.7596 (mmm) REVERT: D 227 GLU cc_start: 0.7576 (tt0) cc_final: 0.6968 (pm20) REVERT: D 243 ASP cc_start: 0.7955 (t0) cc_final: 0.7549 (m-30) REVERT: D 331 THR cc_start: 0.7130 (p) cc_final: 0.6706 (m) REVERT: D 389 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7684 (tp30) REVERT: E 92 LYS cc_start: 0.8620 (tppp) cc_final: 0.8217 (ttmt) REVERT: E 109 LYS cc_start: 0.8241 (tptt) cc_final: 0.7681 (tttp) REVERT: E 124 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6662 (ptm160) REVERT: E 170 ARG cc_start: 0.6590 (ptt-90) cc_final: 0.6022 (mtp85) REVERT: E 196 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7120 (ppp) REVERT: E 265 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7730 (mppt) REVERT: E 279 GLN cc_start: 0.7182 (pt0) cc_final: 0.6083 (tp40) REVERT: E 389 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: E 413 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7559 (mttt) REVERT: E 427 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8215 (ttmm) REVERT: F 147 ASP cc_start: 0.7497 (m-30) cc_final: 0.7217 (p0) REVERT: F 302 ASN cc_start: 0.7789 (t0) cc_final: 0.7386 (t0) REVERT: F 327 ASN cc_start: 0.7347 (p0) cc_final: 0.6852 (p0) REVERT: F 333 LYS cc_start: 0.7454 (ttpp) cc_final: 0.7000 (ttmt) REVERT: F 347 GLU cc_start: 0.7237 (mp0) cc_final: 0.6948 (mm-30) REVERT: F 397 GLU cc_start: 0.6818 (tp30) cc_final: 0.6161 (tm-30) REVERT: F 398 GLN cc_start: 0.7547 (mt0) cc_final: 0.6944 (mp-120) REVERT: F 431 ILE cc_start: 0.7090 (pp) cc_final: 0.6685 (pt) outliers start: 76 outliers final: 37 residues processed: 335 average time/residue: 1.3205 time to fit residues: 501.1305 Evaluate side-chains 320 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 272 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 140 GLN C 288 ASN C 302 ASN D 200 ASN D 279 GLN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21368 Z= 0.177 Angle : 0.504 8.665 28966 Z= 0.266 Chirality : 0.040 0.247 3246 Planarity : 0.003 0.032 3599 Dihedral : 11.069 174.319 2998 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.44 % Allowed : 18.01 % Favored : 78.55 % 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: 0.41 (0.17), residues: 2580 helix: 1.36 (0.15), residues: 1330 sheet: 0.04 (0.29), residues: 340 loop : -1.27 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.005 0.001 HIS B 8 PHE 0.016 0.001 PHE D 65 TYR 0.011 0.001 TYR E 158 ARG 0.004 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 281 time to evaluate : 2.566 Fit side-chains REVERT: A 79 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7915 (mtpm) REVERT: A 203 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7258 (mtmt) REVERT: A 247 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6664 (p0) REVERT: A 333 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.6057 (mmmm) REVERT: A 337 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5742 (mp0) REVERT: A 370 ASP cc_start: 0.6162 (m-30) cc_final: 0.5675 (t70) REVERT: B 57 ASN cc_start: 0.7994 (p0) cc_final: 0.7745 (p0) REVERT: B 96 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8002 (mttt) REVERT: B 231 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: B 270 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7455 (p) REVERT: B 274 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.6904 (mtm-85) REVERT: B 392 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6281 (mp0) REVERT: C 34 LYS cc_start: 0.7627 (tttt) cc_final: 0.7225 (mmtm) REVERT: C 38 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7209 (mtmt) REVERT: C 92 LYS cc_start: 0.8224 (mmmm) cc_final: 0.7798 (mppt) REVERT: C 313 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6421 (pp) REVERT: D 1 MET cc_start: 0.8581 (ptp) cc_final: 0.8206 (ptm) REVERT: D 26 GLU cc_start: 0.7435 (mp0) cc_final: 0.7194 (mp0) REVERT: D 139 ARG cc_start: 0.7373 (ttp80) cc_final: 0.6791 (ttp-110) REVERT: D 153 ASP cc_start: 0.7658 (t0) cc_final: 0.7282 (t70) REVERT: D 226 MET cc_start: 0.7900 (mmm) cc_final: 0.7607 (mmm) REVERT: D 243 ASP cc_start: 0.7973 (t0) cc_final: 0.7572 (m-30) REVERT: D 331 THR cc_start: 0.7263 (p) cc_final: 0.6859 (m) REVERT: D 389 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: E 92 LYS cc_start: 0.8635 (tppp) cc_final: 0.8222 (ttmt) REVERT: E 103 MET cc_start: 0.8170 (mmt) cc_final: 0.7373 (mtp) REVERT: E 109 LYS cc_start: 0.8266 (tptt) cc_final: 0.7703 (tttp) REVERT: E 124 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6653 (ptm160) REVERT: E 170 ARG cc_start: 0.6586 (ptt-90) cc_final: 0.6025 (mtp85) REVERT: E 196 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7153 (ppp) REVERT: E 228 MET cc_start: 0.6219 (mmm) cc_final: 0.5867 (ptt) REVERT: E 265 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7708 (mppt) REVERT: E 279 GLN cc_start: 0.7156 (pt0) cc_final: 0.6094 (tp40) REVERT: E 389 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7385 (tp30) REVERT: E 413 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7534 (mttt) REVERT: E 427 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8229 (ttmm) REVERT: F 147 ASP cc_start: 0.7486 (m-30) cc_final: 0.7220 (p0) REVERT: F 302 ASN cc_start: 0.7776 (t0) cc_final: 0.7372 (t0) REVERT: F 327 ASN cc_start: 0.7328 (p0) cc_final: 0.6869 (p0) REVERT: F 333 LYS cc_start: 0.7381 (ttpp) cc_final: 0.6916 (ttmt) REVERT: F 347 GLU cc_start: 0.7247 (mp0) cc_final: 0.6950 (mm-30) REVERT: F 370 ASP cc_start: 0.6125 (m-30) cc_final: 0.5830 (m-30) REVERT: F 397 GLU cc_start: 0.6837 (tp30) cc_final: 0.6197 (tm-30) REVERT: F 398 GLN cc_start: 0.7561 (mt0) cc_final: 0.7003 (mp-120) REVERT: F 431 ILE cc_start: 0.7074 (pp) cc_final: 0.6698 (pt) outliers start: 77 outliers final: 40 residues processed: 330 average time/residue: 1.3790 time to fit residues: 515.5247 Evaluate side-chains 326 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 274 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 49 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 196 optimal weight: 0.7980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 62 ASN B 140 GLN B 200 ASN C 288 ASN C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21368 Z= 0.132 Angle : 0.485 10.949 28966 Z= 0.255 Chirality : 0.039 0.203 3246 Planarity : 0.003 0.033 3599 Dihedral : 10.904 177.115 2998 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.82 % Allowed : 19.08 % Favored : 78.11 % 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: 0.57 (0.17), residues: 2580 helix: 1.56 (0.15), residues: 1330 sheet: 0.03 (0.29), residues: 341 loop : -1.27 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 89 HIS 0.006 0.001 HIS B 8 PHE 0.012 0.001 PHE B 417 TYR 0.015 0.001 TYR A 312 ARG 0.004 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 288 time to evaluate : 2.561 Fit side-chains REVERT: A 79 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7884 (mtpm) REVERT: A 247 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6688 (p0) REVERT: A 333 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5738 (mmmm) REVERT: A 337 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5631 (mp0) REVERT: A 370 ASP cc_start: 0.6179 (m-30) cc_final: 0.5587 (t70) REVERT: B 57 ASN cc_start: 0.7914 (p0) cc_final: 0.7662 (p0) REVERT: B 96 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7980 (mttt) REVERT: B 140 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6845 (tm-30) REVERT: B 254 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7929 (tp) REVERT: B 270 SER cc_start: 0.7674 (OUTLIER) cc_final: 0.7435 (p) REVERT: B 274 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6881 (mtm-85) REVERT: B 350 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8524 (tt) REVERT: B 392 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6246 (mp0) REVERT: C 92 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7815 (mppt) REVERT: C 128 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6645 (mtt) REVERT: C 140 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7450 (tm130) REVERT: C 313 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6365 (pp) REVERT: D 1 MET cc_start: 0.8596 (ptp) cc_final: 0.8270 (ptm) REVERT: D 26 GLU cc_start: 0.7454 (mp0) cc_final: 0.7233 (mp0) REVERT: D 153 ASP cc_start: 0.7595 (t0) cc_final: 0.7222 (t70) REVERT: D 226 MET cc_start: 0.7879 (mmm) cc_final: 0.7532 (mmm) REVERT: D 243 ASP cc_start: 0.7987 (t0) cc_final: 0.7606 (m-30) REVERT: D 331 THR cc_start: 0.7163 (p) cc_final: 0.6717 (m) REVERT: E 92 LYS cc_start: 0.8527 (tppp) cc_final: 0.8166 (ttmt) REVERT: E 103 MET cc_start: 0.7705 (mmt) cc_final: 0.7435 (mtp) REVERT: E 109 LYS cc_start: 0.8191 (tptt) cc_final: 0.7683 (tttp) REVERT: E 124 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6586 (ptm160) REVERT: E 170 ARG cc_start: 0.6603 (ptt-90) cc_final: 0.6041 (mtp85) REVERT: E 196 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7091 (ppp) REVERT: E 228 MET cc_start: 0.6136 (mmm) cc_final: 0.5750 (ptt) REVERT: E 279 GLN cc_start: 0.7143 (pt0) cc_final: 0.6107 (tm-30) REVERT: E 345 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6268 (tt0) REVERT: E 371 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6863 (tp) REVERT: E 413 LYS cc_start: 0.7745 (ttmt) cc_final: 0.7475 (mttt) REVERT: F 147 ASP cc_start: 0.7453 (m-30) cc_final: 0.7209 (p0) REVERT: F 251 ASP cc_start: 0.6638 (m-30) cc_final: 0.6384 (p0) REVERT: F 296 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: F 302 ASN cc_start: 0.7727 (t0) cc_final: 0.7312 (t0) REVERT: F 327 ASN cc_start: 0.7270 (p0) cc_final: 0.6821 (p0) REVERT: F 333 LYS cc_start: 0.7372 (ttpp) cc_final: 0.6891 (ttmt) REVERT: F 347 GLU cc_start: 0.7254 (mp0) cc_final: 0.6917 (mm-30) REVERT: F 397 GLU cc_start: 0.6847 (tp30) cc_final: 0.6183 (tm-30) REVERT: F 398 GLN cc_start: 0.7504 (mt0) cc_final: 0.7000 (mp-120) REVERT: F 431 ILE cc_start: 0.7035 (pp) cc_final: 0.6656 (pt) outliers start: 63 outliers final: 29 residues processed: 326 average time/residue: 1.3691 time to fit residues: 505.3542 Evaluate side-chains 313 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 270 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 296 GLU Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 218 optimal weight: 0.4980 chunk 232 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 200 ASN C 288 ASN C 302 ASN D 100 GLN D 200 ASN E 125 ASN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21368 Z= 0.148 Angle : 0.494 10.589 28966 Z= 0.258 Chirality : 0.039 0.192 3246 Planarity : 0.003 0.037 3599 Dihedral : 10.845 176.112 2998 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.64 % Allowed : 19.75 % Favored : 77.61 % 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: 0.64 (0.17), residues: 2580 helix: 1.63 (0.15), residues: 1328 sheet: 0.04 (0.30), residues: 343 loop : -1.23 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 162 HIS 0.006 0.001 HIS B 8 PHE 0.013 0.001 PHE D 65 TYR 0.026 0.001 TYR A 312 ARG 0.010 0.000 ARG D 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 278 time to evaluate : 2.385 Fit side-chains REVERT: A 79 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7943 (mtpm) REVERT: A 247 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6756 (p0) REVERT: A 333 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.6045 (mmmm) REVERT: A 337 GLU cc_start: 0.6154 (mt-10) cc_final: 0.5651 (mp0) REVERT: A 370 ASP cc_start: 0.6161 (m-30) cc_final: 0.5574 (t70) REVERT: B 57 ASN cc_start: 0.7916 (p0) cc_final: 0.7667 (p0) REVERT: B 96 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8017 (mttm) REVERT: B 140 GLN cc_start: 0.7029 (tm-30) cc_final: 0.6806 (tm-30) REVERT: B 270 SER cc_start: 0.7707 (OUTLIER) cc_final: 0.7465 (p) REVERT: B 274 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.6949 (mtm-85) REVERT: B 392 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6263 (mp0) REVERT: C 92 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7821 (mppt) REVERT: C 128 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6661 (mtt) REVERT: C 313 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6374 (pp) REVERT: D 1 MET cc_start: 0.8590 (ptp) cc_final: 0.8230 (ptm) REVERT: D 26 GLU cc_start: 0.7499 (mp0) cc_final: 0.7258 (mp0) REVERT: D 139 ARG cc_start: 0.7171 (ttp80) cc_final: 0.6574 (ttp-110) REVERT: D 153 ASP cc_start: 0.7589 (t0) cc_final: 0.7205 (t70) REVERT: D 226 MET cc_start: 0.7885 (mmm) cc_final: 0.7548 (mmm) REVERT: D 243 ASP cc_start: 0.7984 (t0) cc_final: 0.7606 (m-30) REVERT: D 331 THR cc_start: 0.7235 (p) cc_final: 0.6800 (m) REVERT: E 92 LYS cc_start: 0.8518 (tppp) cc_final: 0.8152 (ttmt) REVERT: E 109 LYS cc_start: 0.8192 (tptt) cc_final: 0.7680 (tttp) REVERT: E 124 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6589 (ptm160) REVERT: E 170 ARG cc_start: 0.6692 (ptt-90) cc_final: 0.6157 (mtp85) REVERT: E 196 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7105 (ppp) REVERT: E 228 MET cc_start: 0.6140 (mmm) cc_final: 0.5756 (ptt) REVERT: E 279 GLN cc_start: 0.7133 (pt0) cc_final: 0.6110 (tm-30) REVERT: E 345 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6231 (tt0) REVERT: E 371 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6615 (pt) REVERT: E 413 LYS cc_start: 0.7755 (ttmt) cc_final: 0.7509 (mttt) REVERT: F 147 ASP cc_start: 0.7473 (m-30) cc_final: 0.7233 (p0) REVERT: F 251 ASP cc_start: 0.6683 (m-30) cc_final: 0.6409 (p0) REVERT: F 296 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: F 302 ASN cc_start: 0.7679 (t0) cc_final: 0.7262 (t0) REVERT: F 327 ASN cc_start: 0.7262 (p0) cc_final: 0.6821 (p0) REVERT: F 333 LYS cc_start: 0.7326 (ttpp) cc_final: 0.6973 (ttmt) REVERT: F 347 GLU cc_start: 0.7267 (mp0) cc_final: 0.6922 (mm-30) REVERT: F 370 ASP cc_start: 0.6141 (m-30) cc_final: 0.5857 (m-30) REVERT: F 397 GLU cc_start: 0.6852 (tp30) cc_final: 0.6194 (tm-30) REVERT: F 398 GLN cc_start: 0.7503 (mt0) cc_final: 0.7026 (mp-120) REVERT: F 431 ILE cc_start: 0.7030 (pp) cc_final: 0.6654 (pt) outliers start: 59 outliers final: 31 residues processed: 319 average time/residue: 1.4466 time to fit residues: 521.2763 Evaluate side-chains 309 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 267 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 296 GLU Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 171 optimal weight: 0.0670 chunk 258 optimal weight: 9.9990 chunk 237 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 200 ASN C 288 ASN C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21368 Z= 0.148 Angle : 0.494 11.236 28966 Z= 0.258 Chirality : 0.039 0.189 3246 Planarity : 0.003 0.036 3599 Dihedral : 10.793 176.823 2998 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.37 % Allowed : 20.29 % Favored : 77.35 % 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: 0.69 (0.17), residues: 2580 helix: 1.68 (0.15), residues: 1327 sheet: 0.03 (0.29), residues: 343 loop : -1.22 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 162 HIS 0.007 0.001 HIS B 8 PHE 0.013 0.001 PHE D 65 TYR 0.011 0.001 TYR A 312 ARG 0.008 0.000 ARG D 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 276 time to evaluate : 2.336 Fit side-chains REVERT: A 79 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7948 (mtpm) REVERT: A 247 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6794 (p0) REVERT: A 333 LYS cc_start: 0.6401 (OUTLIER) cc_final: 0.6042 (mmmm) REVERT: A 337 GLU cc_start: 0.6155 (mt-10) cc_final: 0.5635 (mp0) REVERT: A 370 ASP cc_start: 0.6089 (m-30) cc_final: 0.5557 (t70) REVERT: B 57 ASN cc_start: 0.7920 (p0) cc_final: 0.7662 (p0) REVERT: B 96 LYS cc_start: 0.8334 (mtpp) cc_final: 0.8009 (mttm) REVERT: B 140 GLN cc_start: 0.6979 (tm-30) cc_final: 0.6774 (tm-30) REVERT: B 274 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6942 (mtm-85) REVERT: B 392 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6288 (mp0) REVERT: C 92 LYS cc_start: 0.8214 (mmmm) cc_final: 0.7824 (mppt) REVERT: C 128 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6647 (mtt) REVERT: C 313 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6394 (pp) REVERT: D 1 MET cc_start: 0.8588 (ptp) cc_final: 0.8252 (ptm) REVERT: D 26 GLU cc_start: 0.7480 (mp0) cc_final: 0.7236 (mp0) REVERT: D 139 ARG cc_start: 0.7166 (ttp80) cc_final: 0.6576 (ttp-110) REVERT: D 153 ASP cc_start: 0.7567 (t0) cc_final: 0.7317 (t0) REVERT: D 226 MET cc_start: 0.7887 (mmm) cc_final: 0.7550 (mmm) REVERT: D 331 THR cc_start: 0.7243 (p) cc_final: 0.6800 (m) REVERT: E 92 LYS cc_start: 0.8512 (tppp) cc_final: 0.8150 (ttmt) REVERT: E 109 LYS cc_start: 0.8189 (tptt) cc_final: 0.7698 (tttp) REVERT: E 124 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6622 (ptm160) REVERT: E 170 ARG cc_start: 0.6674 (ptt-90) cc_final: 0.6146 (mtp85) REVERT: E 196 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7063 (ppp) REVERT: E 345 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6217 (tt0) REVERT: E 371 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6605 (pt) REVERT: E 413 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7499 (mttt) REVERT: F 147 ASP cc_start: 0.7471 (m-30) cc_final: 0.7229 (p0) REVERT: F 251 ASP cc_start: 0.6675 (m-30) cc_final: 0.6422 (p0) REVERT: F 296 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: F 302 ASN cc_start: 0.7685 (t0) cc_final: 0.7253 (t0) REVERT: F 327 ASN cc_start: 0.7237 (p0) cc_final: 0.6805 (p0) REVERT: F 333 LYS cc_start: 0.7318 (ttpp) cc_final: 0.6967 (ttmt) REVERT: F 347 GLU cc_start: 0.7254 (mp0) cc_final: 0.6881 (mm-30) REVERT: F 370 ASP cc_start: 0.6149 (m-30) cc_final: 0.5862 (m-30) REVERT: F 397 GLU cc_start: 0.6826 (tp30) cc_final: 0.6133 (tm-30) REVERT: F 398 GLN cc_start: 0.7468 (mt0) cc_final: 0.7051 (mp-120) REVERT: F 431 ILE cc_start: 0.7026 (pp) cc_final: 0.6658 (pt) outliers start: 53 outliers final: 33 residues processed: 312 average time/residue: 1.3350 time to fit residues: 472.0339 Evaluate side-chains 308 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 265 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 296 GLU Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 30 optimal weight: 0.0470 chunk 57 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 200 ASN C 288 ASN C 302 ASN D 100 GLN D 200 ASN E 57 ASN E 167 ASN E 200 ASN F 140 GLN F 295 ASN F 359 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145608 restraints weight = 22504.662| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.09 r_work: 0.3458 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21368 Z= 0.144 Angle : 0.488 10.956 28966 Z= 0.255 Chirality : 0.039 0.184 3246 Planarity : 0.003 0.035 3599 Dihedral : 10.749 177.530 2998 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.23 % Allowed : 20.55 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2580 helix: 1.75 (0.15), residues: 1325 sheet: 0.03 (0.29), residues: 343 loop : -1.20 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 154 HIS 0.007 0.001 HIS B 8 PHE 0.013 0.001 PHE D 65 TYR 0.021 0.001 TYR A 312 ARG 0.008 0.000 ARG D 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8915.66 seconds wall clock time: 158 minutes 49.69 seconds (9529.69 seconds total)