Starting phenix.real_space_refine on Mon Mar 18 12:53:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0z_29658/03_2024/8g0z_29658_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0z_29658/03_2024/8g0z_29658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0z_29658/03_2024/8g0z_29658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0z_29658/03_2024/8g0z_29658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0z_29658/03_2024/8g0z_29658_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g0z_29658/03_2024/8g0z_29658_updated.pdb" } resolution = 3.61 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= 0.009 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 3475 2.21 5 O 4074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 389": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: "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: "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: 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: 10.75, per 1000 atoms: 0.51 Number of scatterers: 20944 At special positions: 0 Unit cell: (140.973, 136.857, 143.031, 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 4074 8.00 N 3475 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: 8.28 Conformation dependent library (CDL) restraints added in 3.0 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 47.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 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 205 through 216 removed outlier: 3.636A pdb=" N TYR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 215 " --> pdb=" O ALA A 211 " (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 removed outlier: 4.018A pdb=" N ALA B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) 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 231 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: 3.549A 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: 4.360A pdb=" N GLN E 140 " --> pdb=" O ILE E 137 " (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: 3.842A 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: 3.871A 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 299 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: 3.674A pdb=" N LEU A 400 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 388 " --> pdb=" O LEU A 400 " (cutoff:3.500A) 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: 4.151A 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: 3.627A 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: 6.430A 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: 7.638A pdb=" N SER C 225 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.651A 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: 6.037A 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: 6.345A 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: 7.947A 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: 6.210A pdb=" N ILE D 276 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 7.575A 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: 6.501A 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: 3.556A 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: 7.246A pdb=" N SER E 225 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.276A 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: 7.837A pdb=" N THR F 352 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 6.531A 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 422 852 hydrogen bonds defined for protein. 2424 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: 5.84 Time building geometry restraints manager: 9.01 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: 5604 1.50 - 1.65: 8860 1.65 - 1.80: 95 1.80 - 1.95: 114 Bond restraints: 21368 Sorted by residual: bond pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta sigma weight residual 1.460 1.494 -0.034 8.60e-03 1.35e+04 1.54e+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 1.50e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+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 1.14e+01 bond pdb=" N SER F 225 " pdb=" CA SER F 225 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.25e-02 6.40e+03 1.07e+01 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.53: 581 106.53 - 113.47: 11866 113.47 - 120.40: 8216 120.40 - 127.34: 8079 127.34 - 134.27: 224 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.71 107.76 5.95 9.50e-01 1.11e+00 3.92e+01 angle pdb=" N MET C 226 " pdb=" CA MET C 226 " pdb=" C MET C 226 " ideal model delta sigma weight residual 112.54 107.17 5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.78 -12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" PB AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sigma weight residual 120.12 131.99 -11.87 3.00e+00 1.11e-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 113.80 117.75 -3.95 1.00e+00 1.00e+00 1.56e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 12745 34.84 - 69.67: 174 69.67 - 104.51: 8 104.51 - 139.35: 1 139.35 - 174.18: 3 Dihedral angle restraints: 12931 sinusoidal: 5317 harmonic: 7614 Sorted by residual: 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 -67.73 106.45 -174.18 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 -88.55 157.46 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" O1A AGS D 501 " pdb=" O3A AGS D 501 " pdb=" PA AGS D 501 " pdb=" PB AGS D 501 " ideal model delta sinusoidal sigma weight residual -67.73 66.55 -134.28 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 12928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2317 0.044 - 0.088: 570 0.088 - 0.132: 270 0.132 - 0.176: 66 0.176 - 0.220: 23 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 1.21e+00 chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+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 2.72 -0.21 2.00e-01 2.50e+01 1.13e+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 3.35e-02 1.12e+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 2.26e-02 5.12e+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 SER B 255 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C SER B 255 " 0.038 2.00e-02 2.50e+03 pdb=" O SER B 255 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 256 " -0.013 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 82 2.44 - 3.06: 14292 3.06 - 3.67: 31956 3.67 - 4.29: 49559 4.29 - 4.90: 80866 Nonbonded interactions: 176755 Sorted by model distance: nonbonded pdb=" O3G AGS F 501 " pdb="MG MG F 502 " model vdw 1.829 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 2.157 2.170 nonbonded pdb=" O2B AGS D 501 " pdb="MG MG D 502 " model vdw 2.172 2.170 nonbonded pdb=" O3G AGS C 501 " pdb="MG MG C 502 " model vdw 2.188 2.170 nonbonded pdb=" O LEU C 179 " pdb=" OG1 THR C 183 " model vdw 2.208 2.440 ... (remaining 176750 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 3.070 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 52.370 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 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 : 0.005 0.052 21368 Z= 0.334 Angle : 0.743 12.657 28966 Z= 0.503 Chirality : 0.051 0.220 3246 Planarity : 0.004 0.075 3599 Dihedral : 12.134 174.183 8011 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.19 % Allowed : 6.52 % Favored : 91.29 % 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: 0.25 (0.17), residues: 2580 helix: 1.37 (0.15), residues: 1308 sheet: -0.45 (0.30), residues: 342 loop : -1.31 (0.20), residues: 930 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 0.022 0.002 PHE D 383 TYR 0.014 0.001 TYR E 329 ARG 0.002 0.000 ARG F 291 *********************** 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 484 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 435 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.4830 (OUTLIER) cc_final: 0.4475 (tmmt) REVERT: B 43 HIS cc_start: 0.6384 (t-90) cc_final: 0.6126 (t-90) REVERT: B 155 MET cc_start: 0.6828 (tpp) cc_final: 0.6006 (ptt) REVERT: B 166 MET cc_start: 0.7525 (ptm) cc_final: 0.6853 (tpp) REVERT: D 43 HIS cc_start: 0.6779 (t-90) cc_final: 0.6517 (t-90) REVERT: D 138 MET cc_start: 0.6987 (mmm) cc_final: 0.6743 (mmm) REVERT: D 355 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7159 (mm-40) REVERT: E 228 MET cc_start: 0.7540 (mtm) cc_final: 0.7305 (mtt) REVERT: E 355 GLN cc_start: 0.6268 (mm-40) cc_final: 0.6038 (mm-40) REVERT: E 380 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6463 (p) REVERT: E 388 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6188 (pt) REVERT: F 165 TYR cc_start: 0.6929 (m-10) cc_final: 0.6185 (m-10) REVERT: F 326 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7083 (mm-30) REVERT: F 418 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6322 (mp) REVERT: F 423 LYS cc_start: 0.6995 (mttm) cc_final: 0.6595 (mttp) outliers start: 49 outliers final: 5 residues processed: 474 average time/residue: 0.3256 time to fit residues: 234.8246 Evaluate side-chains 266 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 257 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 418 LEU 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: 10.0000 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 167 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 426 GLN C 114 GLN C 227 GLN D 227 GLN D 403 GLN D 422 GLN F 35 ASN F 43 HIS ** F 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 21368 Z= 0.354 Angle : 0.684 9.425 28966 Z= 0.359 Chirality : 0.046 0.344 3246 Planarity : 0.004 0.043 3599 Dihedral : 10.906 175.983 3013 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.17 % Allowed : 12.24 % Favored : 84.58 % 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: -0.35 (0.17), residues: 2580 helix: 0.73 (0.14), residues: 1328 sheet: -0.65 (0.29), residues: 335 loop : -1.42 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 266 HIS 0.007 0.001 HIS A 8 PHE 0.022 0.003 PHE F 383 TYR 0.036 0.003 TYR C 223 ARG 0.008 0.001 ARG C 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 394 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 323 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.6832 (tpp) cc_final: 0.6434 (tpp) REVERT: A 188 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 263 MET cc_start: 0.6615 (mmm) cc_final: 0.6406 (mmt) REVERT: A 333 LYS cc_start: 0.5254 (OUTLIER) cc_final: 0.4475 (ttpt) REVERT: B 8 HIS cc_start: 0.7490 (m90) cc_final: 0.7215 (m-70) REVERT: B 138 MET cc_start: 0.7171 (mmp) cc_final: 0.6639 (mmm) REVERT: B 166 MET cc_start: 0.7734 (ptm) cc_final: 0.7250 (tpp) REVERT: B 181 LYS cc_start: 0.7450 (pttt) cc_final: 0.7009 (pttt) REVERT: C 168 LYS cc_start: 0.7128 (mptt) cc_final: 0.6324 (mmmt) REVERT: C 204 SER cc_start: 0.8056 (OUTLIER) cc_final: 0.7568 (t) REVERT: C 295 ASN cc_start: 0.6682 (t0) cc_final: 0.6339 (t0) REVERT: D 43 HIS cc_start: 0.7121 (t-90) cc_final: 0.6660 (t-90) REVERT: D 326 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6924 (mm-30) REVERT: E 228 MET cc_start: 0.7655 (mtm) cc_final: 0.7416 (mtt) REVERT: F 112 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: F 155 MET cc_start: 0.6534 (ptt) cc_final: 0.6068 (ptt) REVERT: F 158 TYR cc_start: 0.5175 (p90) cc_final: 0.4944 (p90) REVERT: F 165 TYR cc_start: 0.7215 (m-10) cc_final: 0.6393 (m-10) REVERT: F 326 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7732 (mm-30) REVERT: F 418 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6259 (mp) REVERT: F 423 LYS cc_start: 0.6833 (mttm) cc_final: 0.6603 (mttp) outliers start: 71 outliers final: 34 residues processed: 376 average time/residue: 0.3071 time to fit residues: 182.3752 Evaluate side-chains 304 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 266 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 HIS D 403 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 21368 Z= 0.199 Angle : 0.535 7.327 28966 Z= 0.281 Chirality : 0.041 0.228 3246 Planarity : 0.003 0.039 3599 Dihedral : 10.499 171.619 3008 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.59 % Allowed : 13.81 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2580 helix: 1.00 (0.15), residues: 1314 sheet: -0.76 (0.28), residues: 343 loop : -1.38 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 162 HIS 0.007 0.001 HIS B 43 PHE 0.014 0.002 PHE E 417 TYR 0.017 0.001 TYR A 47 ARG 0.004 0.000 ARG A 170 *********************** 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 324 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 266 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.5625 (OUTLIER) cc_final: 0.5422 (pp20) REVERT: A 128 MET cc_start: 0.6738 (tpp) cc_final: 0.6507 (tpp) REVERT: A 188 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6608 (mt-10) REVERT: A 333 LYS cc_start: 0.5189 (OUTLIER) cc_final: 0.4465 (ttpt) REVERT: B 8 HIS cc_start: 0.7455 (m90) cc_final: 0.7197 (m-70) REVERT: B 43 HIS cc_start: 0.7990 (t-90) cc_final: 0.7588 (t-90) REVERT: B 46 GLU cc_start: 0.6852 (tt0) cc_final: 0.6620 (mt-10) REVERT: B 138 MET cc_start: 0.7356 (mmp) cc_final: 0.7073 (mmm) REVERT: B 166 MET cc_start: 0.7794 (ptm) cc_final: 0.7391 (tpp) REVERT: B 181 LYS cc_start: 0.7499 (pttt) cc_final: 0.7228 (pttt) REVERT: C 168 LYS cc_start: 0.7034 (mptt) cc_final: 0.6229 (mmmt) REVERT: C 226 MET cc_start: 0.7985 (mmp) cc_final: 0.7715 (mmp) REVERT: D 43 HIS cc_start: 0.7047 (t-90) cc_final: 0.6642 (t-90) REVERT: D 263 MET cc_start: 0.6112 (mmp) cc_final: 0.5855 (tpp) REVERT: D 298 LYS cc_start: 0.7381 (mmtt) cc_final: 0.6588 (mtmt) REVERT: D 326 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6963 (mm-30) REVERT: E 80 LEU cc_start: 0.5384 (OUTLIER) cc_final: 0.5109 (mt) REVERT: E 103 MET cc_start: 0.7050 (mmp) cc_final: 0.6397 (mmt) REVERT: E 155 MET cc_start: 0.4353 (tpp) cc_final: 0.4089 (tpt) REVERT: E 158 TYR cc_start: 0.5581 (p90) cc_final: 0.4945 (p90) REVERT: E 223 TYR cc_start: 0.6860 (t80) cc_final: 0.6527 (t80) REVERT: E 228 MET cc_start: 0.7600 (mtm) cc_final: 0.7300 (mtt) REVERT: E 272 LEU cc_start: 0.8091 (tp) cc_final: 0.7701 (tp) REVERT: F 3 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7114 (mm-30) REVERT: F 47 TYR cc_start: 0.7554 (m-80) cc_final: 0.7337 (m-80) REVERT: F 155 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.6131 (ptt) REVERT: F 158 TYR cc_start: 0.5174 (p90) cc_final: 0.4834 (p90) REVERT: F 165 TYR cc_start: 0.7227 (m-10) cc_final: 0.6418 (m-10) REVERT: F 241 MET cc_start: 0.7471 (mtm) cc_final: 0.7252 (mtm) REVERT: F 326 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7730 (mm-30) REVERT: F 423 LYS cc_start: 0.7070 (mttm) cc_final: 0.6557 (mttp) outliers start: 58 outliers final: 28 residues processed: 315 average time/residue: 0.2962 time to fit residues: 150.1003 Evaluate side-chains 276 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN D 13 GLN F 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21368 Z= 0.369 Angle : 0.686 9.370 28966 Z= 0.358 Chirality : 0.046 0.199 3246 Planarity : 0.004 0.037 3599 Dihedral : 10.930 174.107 3004 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.53 % Allowed : 14.88 % Favored : 81.59 % 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: -0.86 (0.16), residues: 2580 helix: 0.40 (0.14), residues: 1307 sheet: -1.28 (0.28), residues: 355 loop : -1.60 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 162 HIS 0.005 0.001 HIS A 8 PHE 0.024 0.003 PHE F 16 TYR 0.034 0.003 TYR D 15 ARG 0.009 0.001 ARG A 170 *********************** 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 436 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 357 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7873 (tpt) cc_final: 0.7627 (mmm) REVERT: A 188 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7253 (mt-10) REVERT: A 333 LYS cc_start: 0.5275 (OUTLIER) cc_final: 0.4503 (ttpt) REVERT: A 373 GLU cc_start: 0.2849 (OUTLIER) cc_final: 0.2554 (mt-10) REVERT: B 118 GLU cc_start: 0.6872 (tt0) cc_final: 0.6038 (mt-10) REVERT: B 138 MET cc_start: 0.7603 (mmp) cc_final: 0.6784 (mmm) REVERT: B 166 MET cc_start: 0.7835 (ptm) cc_final: 0.7633 (tpp) REVERT: C 13 GLN cc_start: 0.7599 (tp40) cc_final: 0.7292 (mm-40) REVERT: C 24 ASP cc_start: 0.8489 (m-30) cc_final: 0.8011 (m-30) REVERT: C 103 MET cc_start: 0.7926 (tpp) cc_final: 0.7648 (mmt) REVERT: C 140 GLN cc_start: 0.7018 (tm-30) cc_final: 0.6794 (tt0) REVERT: C 168 LYS cc_start: 0.7253 (mptt) cc_final: 0.6425 (mmmt) REVERT: C 175 LYS cc_start: 0.8431 (tmtm) cc_final: 0.8041 (tmtt) REVERT: C 204 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7906 (t) REVERT: D 264 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7213 (mt-10) REVERT: D 298 LYS cc_start: 0.7714 (mmtt) cc_final: 0.6839 (mtmt) REVERT: D 326 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6997 (mm-30) REVERT: D 419 MET cc_start: 0.7860 (mmt) cc_final: 0.7550 (mmt) REVERT: D 429 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7666 (m) REVERT: E 23 MET cc_start: 0.7442 (mmp) cc_final: 0.7166 (mmt) REVERT: E 155 MET cc_start: 0.5198 (tpp) cc_final: 0.4773 (tpt) REVERT: E 158 TYR cc_start: 0.5654 (p90) cc_final: 0.5225 (p90) REVERT: E 228 MET cc_start: 0.7910 (mtm) cc_final: 0.7568 (mtt) REVERT: E 371 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.6930 (tp) REVERT: F 3 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7329 (mm-30) REVERT: F 18 LYS cc_start: 0.7298 (tppp) cc_final: 0.7026 (tmtt) REVERT: F 90 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5373 (mm) REVERT: F 158 TYR cc_start: 0.5405 (p90) cc_final: 0.5092 (p90) REVERT: F 423 LYS cc_start: 0.7156 (mttm) cc_final: 0.6580 (mttm) outliers start: 79 outliers final: 42 residues processed: 412 average time/residue: 0.3104 time to fit residues: 200.9862 Evaluate side-chains 342 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 294 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 15 TYR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 318 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 186 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN D 13 GLN D 35 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN F 398 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21368 Z= 0.377 Angle : 0.672 8.198 28966 Z= 0.354 Chirality : 0.046 0.236 3246 Planarity : 0.004 0.059 3599 Dihedral : 10.965 173.259 3003 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.29 % Allowed : 16.98 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2580 helix: 0.30 (0.15), residues: 1287 sheet: -1.55 (0.27), residues: 356 loop : -1.72 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 428 HIS 0.003 0.001 HIS B 219 PHE 0.020 0.003 PHE E 417 TYR 0.030 0.002 TYR F 165 ARG 0.009 0.001 ARG D 340 *********************** 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 437 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 341 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.6492 (t0) REVERT: A 165 TYR cc_start: 0.7823 (m-10) cc_final: 0.7172 (m-10) REVERT: A 188 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7288 (mt-10) REVERT: A 269 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6482 (mtpp) REVERT: A 333 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4457 (ttpt) REVERT: A 373 GLU cc_start: 0.2668 (OUTLIER) cc_final: 0.2401 (mt-10) REVERT: B 118 GLU cc_start: 0.6946 (tt0) cc_final: 0.6183 (mt-10) REVERT: B 138 MET cc_start: 0.7900 (mmp) cc_final: 0.7251 (mmt) REVERT: B 175 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7210 (ttpt) REVERT: B 181 LYS cc_start: 0.7481 (pttt) cc_final: 0.7022 (pptt) REVERT: B 419 MET cc_start: 0.5044 (ttm) cc_final: 0.4749 (ttm) REVERT: C 13 GLN cc_start: 0.7897 (tp40) cc_final: 0.7587 (mm-40) REVERT: C 24 ASP cc_start: 0.8417 (m-30) cc_final: 0.8030 (m-30) REVERT: C 140 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6835 (tt0) REVERT: C 175 LYS cc_start: 0.8539 (tmtm) cc_final: 0.7988 (tmtt) REVERT: C 253 HIS cc_start: 0.8200 (m-70) cc_final: 0.7850 (m-70) REVERT: D 264 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7156 (mt-10) REVERT: D 326 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6951 (mm-30) REVERT: E 23 MET cc_start: 0.7687 (mmp) cc_final: 0.7463 (mmt) REVERT: E 158 TYR cc_start: 0.5724 (p90) cc_final: 0.5403 (p90) REVERT: E 228 MET cc_start: 0.8021 (mtm) cc_final: 0.7716 (mtt) REVERT: E 254 ILE cc_start: 0.7951 (pt) cc_final: 0.7539 (tt) REVERT: E 371 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6793 (tp) REVERT: E 428 TRP cc_start: 0.8010 (m-10) cc_final: 0.7780 (m100) REVERT: F 18 LYS cc_start: 0.7446 (tppp) cc_final: 0.7168 (tmtt) REVERT: F 90 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5490 (mm) REVERT: F 112 GLU cc_start: 0.6958 (mp0) cc_final: 0.6642 (mp0) REVERT: F 158 TYR cc_start: 0.5659 (p90) cc_final: 0.5298 (p90) REVERT: F 326 GLU cc_start: 0.8286 (mp0) cc_final: 0.7877 (mp0) REVERT: F 416 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6554 (mttt) REVERT: F 423 LYS cc_start: 0.7047 (mttm) cc_final: 0.6519 (mttm) outliers start: 96 outliers final: 58 residues processed: 408 average time/residue: 0.3083 time to fit residues: 197.8003 Evaluate side-chains 362 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 296 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 316 CYS Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 416 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN D 253 HIS ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21368 Z= 0.300 Angle : 0.623 14.746 28966 Z= 0.327 Chirality : 0.043 0.213 3246 Planarity : 0.004 0.042 3599 Dihedral : 10.943 170.708 3003 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.75 % Allowed : 18.81 % Favored : 77.44 % 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: -0.95 (0.16), residues: 2580 helix: 0.48 (0.15), residues: 1293 sheet: -1.62 (0.27), residues: 356 loop : -1.72 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 154 HIS 0.004 0.001 HIS F 43 PHE 0.020 0.002 PHE E 11 TYR 0.025 0.002 TYR D 15 ARG 0.008 0.001 ARG D 340 *********************** 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 398 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 314 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.6543 (t0) REVERT: A 57 ASN cc_start: 0.7049 (m-40) cc_final: 0.6546 (m-40) REVERT: A 145 SER cc_start: 0.8705 (m) cc_final: 0.8204 (p) REVERT: A 165 TYR cc_start: 0.7873 (m-10) cc_final: 0.7175 (m-10) REVERT: A 188 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 333 LYS cc_start: 0.5238 (OUTLIER) cc_final: 0.4363 (ttpt) REVERT: A 368 MET cc_start: 0.2471 (ttp) cc_final: 0.2211 (ptt) REVERT: A 373 GLU cc_start: 0.2583 (OUTLIER) cc_final: 0.2344 (mt-10) REVERT: B 19 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8348 (p) REVERT: B 74 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8024 (mmmt) REVERT: B 118 GLU cc_start: 0.7061 (tt0) cc_final: 0.6196 (mt-10) REVERT: B 138 MET cc_start: 0.7903 (mmp) cc_final: 0.7418 (mmm) REVERT: B 175 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7302 (ttpt) REVERT: B 181 LYS cc_start: 0.7693 (pttt) cc_final: 0.7075 (pptt) REVERT: C 13 GLN cc_start: 0.7949 (tp40) cc_final: 0.7600 (mm-40) REVERT: C 24 ASP cc_start: 0.8410 (m-30) cc_final: 0.8033 (m-30) REVERT: C 140 GLN cc_start: 0.7199 (tm-30) cc_final: 0.6818 (tt0) REVERT: C 175 LYS cc_start: 0.8456 (tmtm) cc_final: 0.8037 (tmtt) REVERT: C 253 HIS cc_start: 0.8037 (m-70) cc_final: 0.7672 (m90) REVERT: D 1 MET cc_start: 0.7623 (ppp) cc_final: 0.7220 (ppp) REVERT: D 264 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7163 (mt-10) REVERT: D 326 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6886 (mm-30) REVERT: E 23 MET cc_start: 0.7869 (mmp) cc_final: 0.7621 (mmt) REVERT: E 138 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7780 (mmm) REVERT: E 158 TYR cc_start: 0.5621 (p90) cc_final: 0.5363 (p90) REVERT: E 228 MET cc_start: 0.7964 (mtm) cc_final: 0.7667 (mtt) REVERT: E 371 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6972 (tp) REVERT: E 428 TRP cc_start: 0.8028 (m-10) cc_final: 0.7811 (m100) REVERT: F 18 LYS cc_start: 0.7414 (tppp) cc_final: 0.7197 (tmtt) REVERT: F 90 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5817 (mm) REVERT: F 99 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6446 (tt0) REVERT: F 128 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.5356 (ttm) REVERT: F 158 TYR cc_start: 0.5769 (p90) cc_final: 0.5412 (p90) REVERT: F 228 MET cc_start: 0.6964 (mtp) cc_final: 0.6746 (mtp) REVERT: F 326 GLU cc_start: 0.8372 (mp0) cc_final: 0.7851 (mp0) REVERT: F 358 LYS cc_start: 0.7545 (ttpt) cc_final: 0.7315 (ttmt) REVERT: F 423 LYS cc_start: 0.7022 (mttm) cc_final: 0.6624 (mttm) outliers start: 84 outliers final: 49 residues processed: 373 average time/residue: 0.3173 time to fit residues: 191.8658 Evaluate side-chains 352 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 293 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 210 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21368 Z= 0.217 Angle : 0.582 14.953 28966 Z= 0.303 Chirality : 0.042 0.233 3246 Planarity : 0.003 0.038 3599 Dihedral : 10.719 168.562 3003 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.13 % Allowed : 20.02 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2580 helix: 0.71 (0.15), residues: 1295 sheet: -1.59 (0.27), residues: 346 loop : -1.64 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 20 HIS 0.005 0.001 HIS A 8 PHE 0.019 0.002 PHE E 11 TYR 0.034 0.002 TYR F 165 ARG 0.006 0.000 ARG D 340 *********************** 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 370 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 300 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6354 (mt-10) REVERT: A 54 ASN cc_start: 0.7390 (OUTLIER) cc_final: 0.6600 (t0) REVERT: A 57 ASN cc_start: 0.7032 (m-40) cc_final: 0.6531 (m-40) REVERT: A 165 TYR cc_start: 0.7838 (m-10) cc_final: 0.7194 (m-10) REVERT: A 188 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7208 (mt-10) REVERT: A 333 LYS cc_start: 0.5171 (OUTLIER) cc_final: 0.4342 (ttpt) REVERT: B 74 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7990 (mmmt) REVERT: B 118 GLU cc_start: 0.7125 (tt0) cc_final: 0.6251 (mt-10) REVERT: B 138 MET cc_start: 0.7847 (mmp) cc_final: 0.7342 (mmm) REVERT: B 181 LYS cc_start: 0.7514 (pttt) cc_final: 0.7003 (pptt) REVERT: B 419 MET cc_start: 0.5515 (ttm) cc_final: 0.5080 (ttm) REVERT: C 24 ASP cc_start: 0.8345 (m-30) cc_final: 0.7981 (m-30) REVERT: C 145 SER cc_start: 0.9060 (p) cc_final: 0.8637 (m) REVERT: C 175 LYS cc_start: 0.8469 (tmtm) cc_final: 0.8056 (tmtt) REVERT: C 253 HIS cc_start: 0.8015 (m-70) cc_final: 0.7701 (m90) REVERT: C 294 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7125 (mm) REVERT: D 1 MET cc_start: 0.7568 (ppp) cc_final: 0.7187 (ppp) REVERT: D 264 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7221 (mt-10) REVERT: D 279 GLN cc_start: 0.8032 (tt0) cc_final: 0.7829 (tt0) REVERT: D 326 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6795 (mm-30) REVERT: E 23 MET cc_start: 0.7793 (mmp) cc_final: 0.7576 (mmt) REVERT: E 103 MET cc_start: 0.7393 (mmp) cc_final: 0.7034 (mmp) REVERT: E 138 MET cc_start: 0.8036 (mmt) cc_final: 0.7834 (mmm) REVERT: E 228 MET cc_start: 0.7892 (mtm) cc_final: 0.7586 (mtt) REVERT: E 371 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6977 (tp) REVERT: E 428 TRP cc_start: 0.7968 (m-10) cc_final: 0.7742 (m100) REVERT: F 3 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7190 (mm-30) REVERT: F 18 LYS cc_start: 0.7410 (tppp) cc_final: 0.7198 (tmtt) REVERT: F 90 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5857 (mm) REVERT: F 99 GLN cc_start: 0.6747 (OUTLIER) cc_final: 0.6419 (tt0) REVERT: F 158 TYR cc_start: 0.5736 (p90) cc_final: 0.5387 (p90) REVERT: F 263 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6733 (mmt) outliers start: 70 outliers final: 46 residues processed: 348 average time/residue: 0.2909 time to fit residues: 162.0003 Evaluate side-chains 337 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 284 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 10.0000 chunk 99 optimal weight: 0.0030 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 0.0370 chunk 158 optimal weight: 3.9990 chunk 170 optimal weight: 0.0670 chunk 123 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21368 Z= 0.152 Angle : 0.557 14.015 28966 Z= 0.288 Chirality : 0.040 0.193 3246 Planarity : 0.003 0.036 3599 Dihedral : 10.352 164.815 3003 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.14 % Allowed : 20.82 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2580 helix: 1.10 (0.15), residues: 1295 sheet: -1.28 (0.28), residues: 327 loop : -1.57 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 20 HIS 0.004 0.001 HIS A 8 PHE 0.021 0.002 PHE E 11 TYR 0.026 0.001 TYR F 15 ARG 0.008 0.000 ARG D 340 *********************** 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 344 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 296 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8294 (m) cc_final: 0.8036 (t) REVERT: A 29 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6402 (mt-10) REVERT: A 54 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.6616 (t0) REVERT: A 57 ASN cc_start: 0.7012 (m-40) cc_final: 0.6589 (m-40) REVERT: A 188 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7073 (mt-10) REVERT: A 333 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4290 (ttpt) REVERT: A 373 GLU cc_start: 0.2368 (OUTLIER) cc_final: 0.2140 (mt-10) REVERT: B 74 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7980 (mmmt) REVERT: B 95 GLU cc_start: 0.7965 (tp30) cc_final: 0.7390 (tt0) REVERT: B 118 GLU cc_start: 0.7024 (tt0) cc_final: 0.6095 (mt-10) REVERT: B 155 MET cc_start: 0.8502 (tpp) cc_final: 0.8225 (tpp) REVERT: B 175 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7230 (ttpt) REVERT: B 181 LYS cc_start: 0.7551 (pttt) cc_final: 0.7046 (pptt) REVERT: C 24 ASP cc_start: 0.8205 (m-30) cc_final: 0.7858 (m-30) REVERT: C 145 SER cc_start: 0.8933 (p) cc_final: 0.8544 (m) REVERT: C 175 LYS cc_start: 0.8334 (tmtm) cc_final: 0.7972 (tmtt) REVERT: C 253 HIS cc_start: 0.7959 (m-70) cc_final: 0.7657 (m90) REVERT: C 294 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7238 (mm) REVERT: D 1 MET cc_start: 0.7308 (ppp) cc_final: 0.7105 (ppp) REVERT: D 46 GLU cc_start: 0.7423 (tt0) cc_final: 0.7193 (mt-10) REVERT: D 264 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7240 (mt-10) REVERT: D 326 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6821 (mm-30) REVERT: D 338 GLU cc_start: 0.7753 (tp30) cc_final: 0.6367 (pt0) REVERT: E 155 MET cc_start: 0.3464 (tpt) cc_final: 0.3158 (mmm) REVERT: E 228 MET cc_start: 0.7637 (mtm) cc_final: 0.7393 (mtt) REVERT: F 18 LYS cc_start: 0.7480 (tppp) cc_final: 0.7276 (tmtt) REVERT: F 90 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5731 (mm) REVERT: F 112 GLU cc_start: 0.7330 (mp0) cc_final: 0.6947 (mp0) REVERT: F 158 TYR cc_start: 0.5447 (p90) cc_final: 0.5108 (p90) REVERT: F 263 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6520 (mmt) outliers start: 48 outliers final: 24 residues processed: 334 average time/residue: 0.2948 time to fit residues: 156.0633 Evaluate side-chains 310 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 279 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.0980 chunk 239 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 220 optimal weight: 0.1980 chunk 231 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21368 Z= 0.168 Angle : 0.565 14.770 28966 Z= 0.291 Chirality : 0.041 0.188 3246 Planarity : 0.003 0.036 3599 Dihedral : 10.296 165.440 3003 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.10 % Allowed : 20.55 % 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: -0.19 (0.17), residues: 2580 helix: 1.22 (0.15), residues: 1298 sheet: -1.36 (0.27), residues: 349 loop : -1.52 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 428 HIS 0.004 0.001 HIS A 8 PHE 0.020 0.001 PHE E 11 TYR 0.019 0.001 TYR D 15 ARG 0.008 0.000 ARG D 340 *********************** 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 327 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 280 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8282 (m) cc_final: 0.8020 (t) REVERT: A 54 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6632 (t0) REVERT: A 57 ASN cc_start: 0.6894 (m-40) cc_final: 0.6467 (m-40) REVERT: A 188 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7133 (mt-10) REVERT: A 333 LYS cc_start: 0.5143 (OUTLIER) cc_final: 0.4335 (ttpt) REVERT: B 74 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7991 (mmmt) REVERT: B 95 GLU cc_start: 0.8040 (tp30) cc_final: 0.7481 (tt0) REVERT: B 118 GLU cc_start: 0.7046 (tt0) cc_final: 0.6115 (mt-10) REVERT: B 175 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7288 (ttpt) REVERT: B 181 LYS cc_start: 0.7527 (pttt) cc_final: 0.7012 (pptt) REVERT: C 24 ASP cc_start: 0.8193 (m-30) cc_final: 0.7864 (m-30) REVERT: C 175 LYS cc_start: 0.8264 (tmtm) cc_final: 0.8002 (tmtt) REVERT: C 253 HIS cc_start: 0.7929 (m-70) cc_final: 0.7635 (m90) REVERT: C 294 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7180 (mm) REVERT: C 384 MET cc_start: 0.8235 (ttm) cc_final: 0.7291 (mtp) REVERT: D 46 GLU cc_start: 0.7433 (tt0) cc_final: 0.7211 (mt-10) REVERT: D 264 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7275 (mt-10) REVERT: D 326 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6866 (mm-30) REVERT: E 148 SER cc_start: 0.7611 (p) cc_final: 0.7012 (t) REVERT: E 155 MET cc_start: 0.3685 (tpt) cc_final: 0.3445 (mmm) REVERT: E 228 MET cc_start: 0.7613 (mtm) cc_final: 0.7375 (mtt) REVERT: F 18 LYS cc_start: 0.7528 (tppp) cc_final: 0.7289 (tmtt) REVERT: F 90 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5809 (mm) REVERT: F 112 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: F 158 TYR cc_start: 0.5473 (p90) cc_final: 0.5140 (p90) REVERT: F 263 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6523 (mmt) outliers start: 47 outliers final: 25 residues processed: 316 average time/residue: 0.3080 time to fit residues: 155.9449 Evaluate side-chains 307 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 275 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 258 optimal weight: 8.9990 chunk 237 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21368 Z= 0.178 Angle : 0.575 14.745 28966 Z= 0.295 Chirality : 0.041 0.204 3246 Planarity : 0.003 0.038 3599 Dihedral : 10.221 165.987 2999 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.70 % Allowed : 20.91 % Favored : 77.39 % 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: -0.18 (0.17), residues: 2580 helix: 1.23 (0.15), residues: 1300 sheet: -1.32 (0.28), residues: 343 loop : -1.55 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP E 428 HIS 0.004 0.001 HIS A 8 PHE 0.021 0.002 PHE C 16 TYR 0.022 0.001 TYR F 15 ARG 0.009 0.000 ARG D 340 ********************** 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 320 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 282 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.6997 (OUTLIER) cc_final: 0.6568 (t0) REVERT: A 57 ASN cc_start: 0.6879 (m-40) cc_final: 0.6416 (m-40) REVERT: A 188 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 333 LYS cc_start: 0.5188 (OUTLIER) cc_final: 0.4340 (ttpt) REVERT: B 74 LYS cc_start: 0.8249 (mmmt) cc_final: 0.8000 (mmmt) REVERT: B 95 GLU cc_start: 0.8070 (tp30) cc_final: 0.7504 (tt0) REVERT: B 118 GLU cc_start: 0.7077 (tt0) cc_final: 0.6433 (mt-10) REVERT: B 155 MET cc_start: 0.8584 (tpp) cc_final: 0.8309 (tpp) REVERT: B 175 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7401 (tmmt) REVERT: B 181 LYS cc_start: 0.7512 (pttt) cc_final: 0.7042 (pptt) REVERT: C 24 ASP cc_start: 0.8212 (m-30) cc_final: 0.7870 (m-30) REVERT: C 175 LYS cc_start: 0.8251 (tmtm) cc_final: 0.7785 (tmtt) REVERT: C 253 HIS cc_start: 0.7917 (m-70) cc_final: 0.7653 (m90) REVERT: C 294 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7193 (mm) REVERT: C 384 MET cc_start: 0.8250 (ttm) cc_final: 0.7310 (mtp) REVERT: D 168 LYS cc_start: 0.5203 (mmmt) cc_final: 0.4634 (mmtp) REVERT: D 264 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7273 (mt-10) REVERT: D 326 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6865 (mm-30) REVERT: D 338 GLU cc_start: 0.7971 (tp30) cc_final: 0.6380 (pt0) REVERT: E 148 SER cc_start: 0.7750 (p) cc_final: 0.7169 (t) REVERT: E 155 MET cc_start: 0.3555 (tpt) cc_final: 0.3340 (mmm) REVERT: E 228 MET cc_start: 0.7651 (mtm) cc_final: 0.7413 (mtt) REVERT: F 3 GLU cc_start: 0.7662 (mm-30) cc_final: 0.6540 (tt0) REVERT: F 18 LYS cc_start: 0.7521 (tppp) cc_final: 0.7279 (tmtt) REVERT: F 90 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5794 (mm) REVERT: F 99 GLN cc_start: 0.6676 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: F 112 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: F 124 ARG cc_start: 0.6582 (ptp90) cc_final: 0.6380 (ptp90) REVERT: F 158 TYR cc_start: 0.5476 (p90) cc_final: 0.5151 (p90) REVERT: F 263 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6565 (mmt) outliers start: 38 outliers final: 27 residues processed: 312 average time/residue: 0.3022 time to fit residues: 149.9207 Evaluate side-chains 306 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 271 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 6.9990 chunk 218 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.198877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.184027 restraints weight = 21151.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180590 restraints weight = 29991.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.176993 restraints weight = 27446.016| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.7436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21368 Z= 0.171 Angle : 0.571 14.892 28966 Z= 0.292 Chirality : 0.041 0.245 3246 Planarity : 0.003 0.039 3599 Dihedral : 10.177 165.766 2999 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.83 % Allowed : 20.96 % 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: -0.13 (0.17), residues: 2580 helix: 1.28 (0.15), residues: 1300 sheet: -1.31 (0.28), residues: 348 loop : -1.53 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 154 HIS 0.004 0.001 HIS A 8 PHE 0.021 0.001 PHE C 16 TYR 0.019 0.001 TYR D 15 ARG 0.008 0.000 ARG D 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4193.82 seconds wall clock time: 77 minutes 17.98 seconds (4637.98 seconds total)