Starting phenix.real_space_refine on Wed Mar 20 00:17:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/03_2024/7ztc_14957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/03_2024/7ztc_14957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/03_2024/7ztc_14957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/03_2024/7ztc_14957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/03_2024/7ztc_14957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/03_2024/7ztc_14957_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 168 5.16 5 C 16100 2.51 5 N 4396 2.21 5 O 4972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25652 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "F" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "G" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "H" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2842 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "W" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "X" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Y" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "Z" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 675 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 135 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.05, per 1000 atoms: 0.51 Number of scatterers: 25652 At special positions: 0 Unit cell: (97, 101.85, 285.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 16 15.00 O 4972 8.00 N 4396 7.00 C 16100 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: 10.31 Conformation dependent library (CDL) restraints added in 3.8 seconds 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 32 sheets defined 58.5% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 55 through 58 No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.309A pdb=" N ASP A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 188 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 193 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR A 194 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.527A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 254 through 261 Proline residue: A 258 - end of helix removed outlier: 4.310A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 261' Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 removed outlier: 4.003A pdb=" N LYS A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.680A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.132A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 4.024A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 removed outlier: 3.585A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 Processing helix chain 'B' and resid 55 through 58 No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.515A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 4.326A pdb=" N ASP B 187 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 193 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 194 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.604A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 254 through 261 Proline residue: B 258 - end of helix removed outlier: 4.340A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 261' Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.977A pdb=" N LYS B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.668A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.149A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 4.021A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.645A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 Processing helix chain 'C' and resid 55 through 58 No H-bonds generated for 'chain 'C' and resid 55 through 58' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.308A pdb=" N ASP C 187 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 193 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR C 194 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.526A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 254 through 261 Proline residue: C 258 - end of helix removed outlier: 4.331A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 261' Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.938A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.721A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.108A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.020A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.638A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 370 Processing helix chain 'D' and resid 55 through 58 No H-bonds generated for 'chain 'D' and resid 55 through 58' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.504A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.322A pdb=" N ASP D 187 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 193 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR D 194 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.549A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 254 through 261 Proline residue: D 258 - end of helix removed outlier: 4.344A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 254 through 261' Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 removed outlier: 4.023A pdb=" N LYS D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 No H-bonds generated for 'chain 'D' and resid 290 through 293' Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.669A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.139A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.066A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.619A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.356A pdb=" N ASP E 187 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU E 193 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR E 194 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 215 removed outlier: 3.516A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 254 through 261 Proline residue: E 258 - end of helix removed outlier: 4.339A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 254 through 261' Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 removed outlier: 4.012A pdb=" N LYS E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 293 No H-bonds generated for 'chain 'E' and resid 290 through 293' Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.684A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.124A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 4.095A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 removed outlier: 3.575A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 370 Processing helix chain 'F' and resid 55 through 58 No H-bonds generated for 'chain 'F' and resid 55 through 58' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 182 through 195 removed outlier: 4.306A pdb=" N ASP F 187 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU F 193 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR F 194 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 215 removed outlier: 4.161A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 254 through 261 Proline residue: F 258 - end of helix removed outlier: 4.358A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 254 through 261' Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 284 removed outlier: 4.030A pdb=" N LYS F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 293 No H-bonds generated for 'chain 'F' and resid 290 through 293' Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 318 removed outlier: 3.674A pdb=" N LYS F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.132A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 4.066A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 removed outlier: 3.612A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 370 Processing helix chain 'G' and resid 55 through 58 No H-bonds generated for 'chain 'G' and resid 55 through 58' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 182 through 195 removed outlier: 4.305A pdb=" N ASP G 187 " --> pdb=" O ASP G 184 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU G 193 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR G 194 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 215 removed outlier: 3.536A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 254 through 261 Proline residue: G 258 - end of helix removed outlier: 4.305A pdb=" N LEU G 261 " --> pdb=" O CYS G 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 254 through 261' Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 284 removed outlier: 4.037A pdb=" N LYS G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 293 No H-bonds generated for 'chain 'G' and resid 290 through 293' Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 318 removed outlier: 3.639A pdb=" N LYS G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.105A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 354 removed outlier: 4.034A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 365 removed outlier: 3.590A pdb=" N GLU G 364 " --> pdb=" O GLN G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 370 Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 182 through 195 removed outlier: 4.279A pdb=" N ASP H 187 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU H 193 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR H 194 " --> pdb=" O LYS H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 215 removed outlier: 3.561A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 254 through 261 Proline residue: H 258 - end of helix removed outlier: 4.340A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 254 through 261' Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 284 removed outlier: 4.017A pdb=" N LYS H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 293 No H-bonds generated for 'chain 'H' and resid 290 through 293' Processing helix chain 'H' and resid 302 through 305 Processing helix chain 'H' and resid 309 through 318 removed outlier: 3.671A pdb=" N LYS H 315 " --> pdb=" O ASP H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 348 removed outlier: 5.161A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 354 removed outlier: 4.042A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 365 removed outlier: 3.566A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 370 Processing helix chain 'W' and resid 3 through 134 Processing helix chain 'X' and resid 3 through 133 Processing helix chain 'Y' and resid 2 through 132 Processing helix chain 'Z' and resid 2 through 133 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.910A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ALA A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 160 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.884A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 160 through 165 Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.857A pdb=" N VAL C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ALA C 135 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 160 through 165 Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.838A pdb=" N VAL D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA D 135 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 18 " --> pdb=" O ASP D 11 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.601A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.910A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ALA E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.543A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.838A pdb=" N VAL F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA F 135 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N VAL F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 34 through 38 Processing sheet with id= W, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.573A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Y, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.912A pdb=" N VAL G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA G 135 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS G 18 " --> pdb=" O ASP G 11 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 34 through 38 Processing sheet with id= AA, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.546A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N MET G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 238 through 241 Processing sheet with id= AC, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.850A pdb=" N VAL H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ALA H 135 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS H 18 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 34 through 38 Processing sheet with id= AE, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.538A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N MET H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 238 through 241 removed outlier: 3.623A pdb=" N LYS H 238 " --> pdb=" O ILE H 250 " (cutoff:3.500A) 1250 hydrogen bonds defined for protein. 3123 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: 8.89 Time building geometry restraints manager: 11.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8434 1.34 - 1.46: 3156 1.46 - 1.57: 14250 1.57 - 1.69: 24 1.69 - 1.81: 296 Bond restraints: 26160 Sorted by residual: bond pdb=" CD1 TYR C 169 " pdb=" CE1 TYR C 169 " ideal model delta sigma weight residual 1.382 1.338 0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CD1 TYR H 169 " pdb=" CE1 TYR H 169 " ideal model delta sigma weight residual 1.382 1.341 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CD1 TYR F 169 " pdb=" CE1 TYR F 169 " ideal model delta sigma weight residual 1.382 1.341 0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB TYR C 169 " pdb=" CG TYR C 169 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.20e-02 2.07e+03 1.80e+00 bond pdb=" CB THR C 160 " pdb=" CG2 THR C 160 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 26155 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.90: 769 105.90 - 113.40: 14271 113.40 - 120.91: 11964 120.91 - 128.42: 8429 128.42 - 135.93: 175 Bond angle restraints: 35608 Sorted by residual: angle pdb=" CA TYR F 169 " pdb=" CB TYR F 169 " pdb=" CG TYR F 169 " ideal model delta sigma weight residual 113.90 104.27 9.63 1.80e+00 3.09e-01 2.86e+01 angle pdb=" N GLY D 42 " pdb=" CA GLY D 42 " pdb=" C GLY D 42 " ideal model delta sigma weight residual 113.18 125.53 -12.35 2.37e+00 1.78e-01 2.72e+01 angle pdb=" N GLY E 42 " pdb=" CA GLY E 42 " pdb=" C GLY E 42 " ideal model delta sigma weight residual 113.18 125.00 -11.82 2.37e+00 1.78e-01 2.49e+01 angle pdb=" N GLY F 42 " pdb=" CA GLY F 42 " pdb=" C GLY F 42 " ideal model delta sigma weight residual 113.18 124.90 -11.72 2.37e+00 1.78e-01 2.45e+01 angle pdb=" CA TYR E 169 " pdb=" CB TYR E 169 " pdb=" CG TYR E 169 " ideal model delta sigma weight residual 113.90 105.66 8.24 1.80e+00 3.09e-01 2.09e+01 ... (remaining 35603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 15414 32.80 - 65.60: 268 65.60 - 98.40: 32 98.40 - 131.19: 8 131.19 - 163.99: 6 Dihedral angle restraints: 15728 sinusoidal: 5688 harmonic: 10040 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.99 -163.99 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.41 -163.41 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O2A ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PA ADP H 401 " pdb=" PB ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.19 -163.19 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 15725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2844 0.046 - 0.093: 894 0.093 - 0.139: 313 0.139 - 0.185: 22 0.185 - 0.231: 11 Chirality restraints: 4084 Sorted by residual: chirality pdb=" CA GLN B 49 " pdb=" N GLN B 49 " pdb=" C GLN B 49 " pdb=" CB GLN B 49 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE C 124 " pdb=" N PHE C 124 " pdb=" C PHE C 124 " pdb=" CB PHE C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE E 124 " pdb=" N PHE E 124 " pdb=" C PHE E 124 " pdb=" CB PHE E 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4081 not shown) Planarity restraints: 4600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 169 " 0.044 2.00e-02 2.50e+03 2.80e-02 1.56e+01 pdb=" CG TYR F 169 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR F 169 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR F 169 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 169 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR F 169 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 169 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 169 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 169 " 0.038 2.00e-02 2.50e+03 2.70e-02 1.46e+01 pdb=" CG TYR E 169 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR E 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 169 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 169 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 169 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 169 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.008 2.00e-02 2.50e+03 2.69e-02 1.45e+01 pdb=" CG TYR A 166 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " -0.037 2.00e-02 2.50e+03 ... (remaining 4597 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 349 2.68 - 3.23: 26097 3.23 - 3.79: 38810 3.79 - 4.34: 51370 4.34 - 4.90: 84437 Nonbonded interactions: 201063 Sorted by model distance: nonbonded pdb=" OG1 THR C 160 " pdb=" O LEU C 178 " model vdw 2.123 2.440 nonbonded pdb=" OG1 THR G 160 " pdb=" O LEU G 178 " model vdw 2.133 2.440 nonbonded pdb=" OG1 THR D 160 " pdb=" O LEU D 178 " model vdw 2.133 2.440 nonbonded pdb=" OG1 THR B 160 " pdb=" O LEU B 178 " model vdw 2.147 2.440 nonbonded pdb=" OG1 THR F 160 " pdb=" O LEU F 178 " model vdw 2.148 2.440 ... (remaining 201058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.030 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 68.030 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.220 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26160 Z= 0.230 Angle : 0.845 12.349 35608 Z= 0.441 Chirality : 0.050 0.231 4084 Planarity : 0.010 0.124 4600 Dihedral : 13.851 163.992 9256 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 2904 helix: -2.50 (0.12), residues: 1096 sheet: -0.67 (0.23), residues: 496 loop : -0.59 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 356 HIS 0.009 0.002 HIS G 87 PHE 0.017 0.001 PHE E 124 TYR 0.064 0.006 TYR E 169 ARG 0.027 0.004 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8866 (mmp) cc_final: 0.8613 (mmp) REVERT: C 44 MET cc_start: 0.7984 (tpt) cc_final: 0.7213 (ttp) REVERT: C 75 ILE cc_start: 0.8704 (mt) cc_final: 0.8255 (tt) REVERT: C 208 ILE cc_start: 0.9168 (mm) cc_final: 0.8946 (mt) REVERT: D 44 MET cc_start: 0.8187 (tpt) cc_final: 0.7245 (ttt) REVERT: D 305 MET cc_start: 0.8378 (mmm) cc_final: 0.7957 (mmt) REVERT: E 9 VAL cc_start: 0.8998 (t) cc_final: 0.8723 (m) REVERT: E 44 MET cc_start: 0.8287 (tpt) cc_final: 0.7862 (tpt) REVERT: E 205 GLU cc_start: 0.7820 (tt0) cc_final: 0.7479 (tt0) REVERT: E 360 GLN cc_start: 0.8240 (mm110) cc_final: 0.7822 (tp40) REVERT: F 24 ASP cc_start: 0.7170 (t0) cc_final: 0.6906 (m-30) REVERT: F 25 ASP cc_start: 0.8104 (t70) cc_final: 0.7527 (t0) REVERT: F 44 MET cc_start: 0.8163 (tpt) cc_final: 0.7808 (tpt) REVERT: F 205 GLU cc_start: 0.7953 (tt0) cc_final: 0.7659 (mt-10) REVERT: F 313 MET cc_start: 0.8887 (tpp) cc_final: 0.8637 (ttp) REVERT: G 43 VAL cc_start: 0.9032 (m) cc_final: 0.8777 (p) REVERT: G 65 LEU cc_start: 0.8918 (mp) cc_final: 0.8630 (mp) REVERT: G 92 ASN cc_start: 0.8140 (t0) cc_final: 0.7865 (m-40) REVERT: H 129 THR cc_start: 0.8152 (p) cc_final: 0.7666 (p) REVERT: H 201 THR cc_start: 0.8361 (m) cc_final: 0.8115 (t) REVERT: H 272 CYS cc_start: 0.7644 (m) cc_final: 0.7240 (m) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.3647 time to fit residues: 349.3788 Evaluate side-chains 288 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.3980 chunk 257 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 266 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 308 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 87 HIS A 88 HIS B 87 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 88 HIS C 296 ASN C 354 GLN D 87 HIS D 88 HIS D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS E 101 HIS E 173 HIS E 252 ASN E 263 GLN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 HIS ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS F 246 GLN G 87 HIS H 87 HIS H 88 HIS H 173 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26160 Z= 0.194 Angle : 0.639 8.787 35608 Z= 0.310 Chirality : 0.044 0.203 4084 Planarity : 0.004 0.039 4600 Dihedral : 9.768 152.331 3792 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.10 % Allowed : 7.97 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 2904 helix: -0.82 (0.14), residues: 1088 sheet: -0.02 (0.23), residues: 496 loop : -0.06 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 356 HIS 0.006 0.001 HIS B 87 PHE 0.032 0.002 PHE C 124 TYR 0.052 0.002 TYR F 169 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 326 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8464 (mmm) cc_final: 0.8108 (mmm) REVERT: A 283 MET cc_start: 0.8763 (mmp) cc_final: 0.8336 (mmm) REVERT: B 169 TYR cc_start: 0.8254 (m-80) cc_final: 0.8039 (m-80) REVERT: B 283 MET cc_start: 0.9194 (mmt) cc_final: 0.8795 (mmt) REVERT: B 288 ASP cc_start: 0.7551 (p0) cc_final: 0.7233 (t0) REVERT: B 291 LYS cc_start: 0.8195 (tttp) cc_final: 0.7336 (mttt) REVERT: C 75 ILE cc_start: 0.8886 (mt) cc_final: 0.8290 (tt) REVERT: C 82 MET cc_start: 0.8097 (mmm) cc_final: 0.7645 (tpt) REVERT: D 44 MET cc_start: 0.8247 (tpt) cc_final: 0.7504 (ttt) REVERT: D 82 MET cc_start: 0.8296 (mmm) cc_final: 0.7929 (tmm) REVERT: D 205 GLU cc_start: 0.7320 (tt0) cc_final: 0.6937 (pt0) REVERT: D 305 MET cc_start: 0.8374 (mmm) cc_final: 0.8009 (mmt) REVERT: E 360 GLN cc_start: 0.8074 (mm110) cc_final: 0.7844 (tp40) REVERT: F 25 ASP cc_start: 0.8192 (t70) cc_final: 0.7567 (t0) REVERT: F 205 GLU cc_start: 0.8046 (tt0) cc_final: 0.7693 (mt-10) REVERT: F 276 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7789 (tp30) REVERT: F 305 MET cc_start: 0.8670 (mmm) cc_final: 0.8468 (mtp) REVERT: F 313 MET cc_start: 0.8833 (tpp) cc_final: 0.8432 (ttt) REVERT: G 115 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8411 (t0) REVERT: G 300 SER cc_start: 0.8765 (t) cc_final: 0.8335 (m) REVERT: H 270 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6932 (mt-10) outliers start: 52 outliers final: 26 residues processed: 365 average time/residue: 0.3172 time to fit residues: 191.4838 Evaluate side-chains 283 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 256 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 107 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 chunk 309 optimal weight: 30.0000 chunk 334 optimal weight: 30.0000 chunk 275 optimal weight: 0.9980 chunk 306 optimal weight: 40.0000 chunk 105 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS D 49 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26160 Z= 0.206 Angle : 0.605 8.146 35608 Z= 0.290 Chirality : 0.043 0.198 4084 Planarity : 0.004 0.051 4600 Dihedral : 8.986 148.404 3792 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.10 % Allowed : 10.28 % Favored : 87.62 % 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: -0.33 (0.15), residues: 2904 helix: -0.35 (0.15), residues: 1056 sheet: 0.04 (0.22), residues: 496 loop : -0.00 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 356 HIS 0.006 0.001 HIS G 371 PHE 0.030 0.002 PHE F 124 TYR 0.029 0.002 TYR H 169 ARG 0.003 0.000 ARG G 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 278 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8546 (mmm) cc_final: 0.8254 (mmm) REVERT: A 123 MET cc_start: 0.8423 (tpp) cc_final: 0.8082 (tpp) REVERT: A 283 MET cc_start: 0.8740 (mmp) cc_final: 0.8189 (mmm) REVERT: B 123 MET cc_start: 0.8509 (tpp) cc_final: 0.8166 (tpp) REVERT: B 288 ASP cc_start: 0.7497 (p0) cc_final: 0.7234 (t0) REVERT: B 291 LYS cc_start: 0.8212 (tttp) cc_final: 0.7468 (mptt) REVERT: D 44 MET cc_start: 0.8352 (tpt) cc_final: 0.7765 (ttt) REVERT: D 305 MET cc_start: 0.8514 (mmm) cc_final: 0.8111 (mmt) REVERT: E 44 MET cc_start: 0.8201 (tpt) cc_final: 0.7967 (tpt) REVERT: E 227 MET cc_start: 0.8607 (mmm) cc_final: 0.8236 (mmm) REVERT: E 355 MET cc_start: 0.8140 (mtp) cc_final: 0.7844 (mtt) REVERT: F 25 ASP cc_start: 0.7854 (t70) cc_final: 0.7545 (t0) REVERT: F 205 GLU cc_start: 0.8070 (tt0) cc_final: 0.7599 (mt-10) REVERT: F 313 MET cc_start: 0.8866 (tpp) cc_final: 0.8442 (ttt) REVERT: G 82 MET cc_start: 0.8652 (mmm) cc_final: 0.8225 (mmm) REVERT: G 92 ASN cc_start: 0.8542 (t0) cc_final: 0.7725 (m-40) REVERT: G 300 SER cc_start: 0.8852 (t) cc_final: 0.8490 (m) outliers start: 52 outliers final: 33 residues processed: 315 average time/residue: 0.3021 time to fit residues: 161.2904 Evaluate side-chains 258 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 225 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 40.0000 chunk 232 optimal weight: 0.4980 chunk 160 optimal weight: 6.9990 chunk 34 optimal weight: 0.0020 chunk 147 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 310 optimal weight: 40.0000 chunk 328 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 294 optimal weight: 20.0000 chunk 88 optimal weight: 0.0980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN C 354 GLN D 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN G 173 HIS H 101 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26160 Z= 0.145 Angle : 0.566 7.539 35608 Z= 0.265 Chirality : 0.042 0.182 4084 Planarity : 0.004 0.051 4600 Dihedral : 8.243 156.073 3792 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.86 % Allowed : 11.00 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 2904 helix: 0.04 (0.16), residues: 1056 sheet: -0.02 (0.21), residues: 496 loop : -0.01 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 86 HIS 0.005 0.001 HIS G 371 PHE 0.032 0.001 PHE A 124 TYR 0.023 0.001 TYR B 362 ARG 0.002 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 280 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8628 (mmm) cc_final: 0.8343 (mmm) REVERT: A 123 MET cc_start: 0.8401 (tpp) cc_final: 0.8147 (tpp) REVERT: A 283 MET cc_start: 0.8669 (mmp) cc_final: 0.8156 (mmm) REVERT: B 123 MET cc_start: 0.8491 (tpp) cc_final: 0.8214 (tpp) REVERT: B 291 LYS cc_start: 0.8059 (tttp) cc_final: 0.7388 (mptt) REVERT: B 316 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7818 (mm-30) REVERT: D 44 MET cc_start: 0.8340 (tpt) cc_final: 0.7827 (ttt) REVERT: D 82 MET cc_start: 0.8452 (mmm) cc_final: 0.8121 (tmm) REVERT: D 305 MET cc_start: 0.8480 (mmm) cc_final: 0.8046 (mmt) REVERT: E 16 MET cc_start: 0.7528 (ptp) cc_final: 0.7311 (ptp) REVERT: E 44 MET cc_start: 0.8235 (tpt) cc_final: 0.7882 (tpt) REVERT: E 355 MET cc_start: 0.8079 (mtp) cc_final: 0.7802 (mtt) REVERT: F 25 ASP cc_start: 0.7804 (t70) cc_final: 0.7539 (t0) REVERT: G 82 MET cc_start: 0.8693 (mmm) cc_final: 0.8392 (mmm) REVERT: G 92 ASN cc_start: 0.8442 (t0) cc_final: 0.7708 (m-40) REVERT: G 205 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: G 300 SER cc_start: 0.8812 (t) cc_final: 0.8452 (m) REVERT: H 82 MET cc_start: 0.8249 (mmm) cc_final: 0.7581 (tmm) outliers start: 46 outliers final: 30 residues processed: 314 average time/residue: 0.3067 time to fit residues: 162.8462 Evaluate side-chains 264 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 234 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 294 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 252 ASN A 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26160 Z= 0.262 Angle : 0.641 9.608 35608 Z= 0.307 Chirality : 0.045 0.224 4084 Planarity : 0.004 0.052 4600 Dihedral : 7.992 175.631 3792 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.71 % Allowed : 11.25 % Favored : 86.04 % 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: -0.33 (0.15), residues: 2904 helix: -0.08 (0.16), residues: 1056 sheet: -0.09 (0.21), residues: 496 loop : -0.21 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 86 HIS 0.005 0.001 HIS G 88 PHE 0.043 0.002 PHE E 124 TYR 0.024 0.002 TYR B 362 ARG 0.002 0.000 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 243 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8605 (t0) REVERT: A 82 MET cc_start: 0.8692 (mmm) cc_final: 0.8360 (mmm) REVERT: A 123 MET cc_start: 0.8429 (tpp) cc_final: 0.8039 (tpp) REVERT: A 283 MET cc_start: 0.8738 (mmp) cc_final: 0.8471 (mmp) REVERT: A 305 MET cc_start: 0.8068 (mtp) cc_final: 0.7825 (mtt) REVERT: B 123 MET cc_start: 0.8520 (tpp) cc_final: 0.8219 (tpp) REVERT: B 291 LYS cc_start: 0.8095 (tttp) cc_final: 0.7395 (mttt) REVERT: D 305 MET cc_start: 0.8543 (mmm) cc_final: 0.8146 (mmt) REVERT: E 44 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7819 (tpt) REVERT: E 82 MET cc_start: 0.8704 (tmm) cc_final: 0.8338 (tpt) REVERT: E 355 MET cc_start: 0.8160 (mtp) cc_final: 0.7885 (mtt) REVERT: F 25 ASP cc_start: 0.7760 (t70) cc_final: 0.7489 (t0) REVERT: F 313 MET cc_start: 0.8914 (mmm) cc_final: 0.8418 (ttt) REVERT: G 82 MET cc_start: 0.8684 (mmm) cc_final: 0.8122 (tmm) REVERT: G 205 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: G 300 SER cc_start: 0.8875 (t) cc_final: 0.8569 (m) REVERT: H 269 MET cc_start: 0.7429 (mtm) cc_final: 0.7084 (ptp) outliers start: 67 outliers final: 48 residues processed: 293 average time/residue: 0.3061 time to fit residues: 153.0208 Evaluate side-chains 270 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 219 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 212 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 0.6980 chunk 295 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 328 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN A 252 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN D 173 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26160 Z= 0.285 Angle : 0.654 11.432 35608 Z= 0.313 Chirality : 0.045 0.229 4084 Planarity : 0.004 0.052 4600 Dihedral : 7.746 171.013 3792 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.71 % Allowed : 11.41 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2904 helix: -0.29 (0.16), residues: 1056 sheet: -0.27 (0.20), residues: 496 loop : -0.39 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 79 HIS 0.006 0.001 HIS G 88 PHE 0.042 0.002 PHE E 124 TYR 0.022 0.002 TYR B 362 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 231 time to evaluate : 3.037 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8691 (mmm) cc_final: 0.8459 (mmm) REVERT: B 47 MET cc_start: 0.5179 (tpp) cc_final: 0.4888 (tpt) REVERT: B 123 MET cc_start: 0.8541 (tpp) cc_final: 0.8248 (tpp) REVERT: B 291 LYS cc_start: 0.8208 (tttp) cc_final: 0.7491 (mptt) REVERT: D 82 MET cc_start: 0.8588 (mmm) cc_final: 0.8214 (tmm) REVERT: D 305 MET cc_start: 0.8459 (mmm) cc_final: 0.8148 (mmt) REVERT: E 82 MET cc_start: 0.8749 (mmm) cc_final: 0.8402 (tpt) REVERT: F 25 ASP cc_start: 0.7628 (t70) cc_final: 0.7384 (t0) REVERT: G 82 MET cc_start: 0.8789 (mmm) cc_final: 0.8075 (tmm) REVERT: G 300 SER cc_start: 0.8907 (t) cc_final: 0.8559 (m) REVERT: H 82 MET cc_start: 0.8599 (mmm) cc_final: 0.8249 (tmm) REVERT: H 269 MET cc_start: 0.7452 (mtm) cc_final: 0.7104 (ptp) outliers start: 67 outliers final: 57 residues processed: 280 average time/residue: 0.3059 time to fit residues: 147.3261 Evaluate side-chains 270 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 213 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 282 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 0.5980 chunk 276 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 327 optimal weight: 30.0000 chunk 205 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26160 Z= 0.169 Angle : 0.586 10.808 35608 Z= 0.273 Chirality : 0.042 0.185 4084 Planarity : 0.004 0.050 4600 Dihedral : 6.812 149.265 3792 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.98 % Allowed : 12.62 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 2904 helix: -0.05 (0.16), residues: 1056 sheet: -0.28 (0.20), residues: 496 loop : -0.36 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 356 HIS 0.006 0.001 HIS G 371 PHE 0.041 0.001 PHE E 124 TYR 0.019 0.001 TYR E 169 ARG 0.002 0.000 ARG F 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 2.795 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8033 (t0) cc_final: 0.7731 (t0) REVERT: A 82 MET cc_start: 0.8684 (mmm) cc_final: 0.8270 (mmm) REVERT: A 283 MET cc_start: 0.8633 (mmp) cc_final: 0.8185 (mmm) REVERT: B 47 MET cc_start: 0.5310 (tpp) cc_final: 0.5061 (tpt) REVERT: B 123 MET cc_start: 0.8411 (tpp) cc_final: 0.8193 (tpp) REVERT: B 283 MET cc_start: 0.8897 (mmt) cc_final: 0.8456 (mmt) REVERT: B 291 LYS cc_start: 0.8077 (tttp) cc_final: 0.7421 (mptt) REVERT: C 132 MET cc_start: 0.8605 (ppp) cc_final: 0.8294 (ppp) REVERT: D 82 MET cc_start: 0.8512 (mmm) cc_final: 0.8246 (tmm) REVERT: D 305 MET cc_start: 0.8384 (mmm) cc_final: 0.8048 (mmt) REVERT: E 82 MET cc_start: 0.8673 (mmm) cc_final: 0.8345 (tpt) REVERT: E 355 MET cc_start: 0.8053 (mtp) cc_final: 0.7730 (mtt) REVERT: F 25 ASP cc_start: 0.7667 (t70) cc_final: 0.7415 (t0) REVERT: G 82 MET cc_start: 0.8761 (mmm) cc_final: 0.8082 (tmm) REVERT: G 283 MET cc_start: 0.8571 (mmp) cc_final: 0.8225 (mmp) REVERT: G 300 SER cc_start: 0.8791 (t) cc_final: 0.8526 (m) REVERT: H 269 MET cc_start: 0.7343 (mtm) cc_final: 0.7075 (ptp) outliers start: 49 outliers final: 33 residues processed: 267 average time/residue: 0.3045 time to fit residues: 139.8078 Evaluate side-chains 254 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 272 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26160 Z= 0.293 Angle : 0.661 13.342 35608 Z= 0.315 Chirality : 0.045 0.238 4084 Planarity : 0.004 0.050 4600 Dihedral : 6.889 141.975 3792 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.43 % Allowed : 12.66 % Favored : 84.91 % 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: -0.72 (0.15), residues: 2904 helix: -0.25 (0.16), residues: 1056 sheet: -0.36 (0.21), residues: 496 loop : -0.56 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 79 HIS 0.005 0.001 HIS C 275 PHE 0.042 0.002 PHE E 124 TYR 0.041 0.002 TYR F 169 ARG 0.003 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 216 time to evaluate : 2.824 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8743 (mmm) cc_final: 0.8524 (mmm) REVERT: B 12 ASN cc_start: 0.9016 (t0) cc_final: 0.8779 (m-40) REVERT: B 123 MET cc_start: 0.8520 (tpp) cc_final: 0.8240 (tpp) REVERT: B 132 MET cc_start: 0.7976 (ttp) cc_final: 0.7517 (pmm) REVERT: B 291 LYS cc_start: 0.8280 (tttp) cc_final: 0.7534 (mptt) REVERT: C 132 MET cc_start: 0.8617 (ppp) cc_final: 0.8269 (ppp) REVERT: D 305 MET cc_start: 0.8449 (mmm) cc_final: 0.8157 (mmt) REVERT: E 82 MET cc_start: 0.8795 (mmm) cc_final: 0.8515 (tpt) REVERT: E 355 MET cc_start: 0.8056 (mtp) cc_final: 0.7737 (mtt) REVERT: F 25 ASP cc_start: 0.7534 (t70) cc_final: 0.7329 (t0) REVERT: G 82 MET cc_start: 0.8803 (mmm) cc_final: 0.8058 (tmm) REVERT: G 300 SER cc_start: 0.8872 (t) cc_final: 0.8575 (m) REVERT: H 82 MET cc_start: 0.8643 (tmm) cc_final: 0.8098 (tmm) outliers start: 60 outliers final: 51 residues processed: 259 average time/residue: 0.3468 time to fit residues: 155.9315 Evaluate side-chains 261 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 16 MET Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 272 CYS Chi-restraints excluded: chain H residue 282 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 30.0000 chunk 313 optimal weight: 30.0000 chunk 286 optimal weight: 9.9990 chunk 305 optimal weight: 40.0000 chunk 183 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 275 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 304 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN D 101 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS F 161 HIS ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 26160 Z= 0.419 Angle : 0.747 14.098 35608 Z= 0.364 Chirality : 0.048 0.254 4084 Planarity : 0.005 0.055 4600 Dihedral : 7.307 149.922 3792 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.71 % Allowed : 12.58 % Favored : 84.71 % 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: -1.23 (0.15), residues: 2904 helix: -0.48 (0.16), residues: 1008 sheet: -0.52 (0.21), residues: 496 loop : -1.09 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 79 HIS 0.008 0.001 HIS C 275 PHE 0.046 0.002 PHE E 124 TYR 0.040 0.002 TYR F 169 ARG 0.004 0.001 ARG F 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 211 time to evaluate : 2.873 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8684 (mmm) cc_final: 0.8273 (mmm) REVERT: B 47 MET cc_start: 0.5124 (tpp) cc_final: 0.4446 (tpt) REVERT: B 123 MET cc_start: 0.8558 (tpp) cc_final: 0.8256 (tpp) REVERT: C 132 MET cc_start: 0.8737 (ppp) cc_final: 0.8372 (ppp) REVERT: D 82 MET cc_start: 0.8641 (mmm) cc_final: 0.8167 (tmm) REVERT: D 305 MET cc_start: 0.8438 (mmm) cc_final: 0.8075 (mmt) REVERT: E 82 MET cc_start: 0.8834 (mmm) cc_final: 0.8559 (tpt) REVERT: E 259 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8540 (tm-30) REVERT: E 355 MET cc_start: 0.8140 (mtp) cc_final: 0.7877 (mtt) REVERT: F 272 CYS cc_start: 0.6717 (m) cc_final: 0.6371 (m) REVERT: G 82 MET cc_start: 0.8857 (mmm) cc_final: 0.8019 (tmm) REVERT: G 300 SER cc_start: 0.8847 (t) cc_final: 0.8547 (m) REVERT: H 82 MET cc_start: 0.8712 (mmm) cc_final: 0.8245 (tmm) outliers start: 67 outliers final: 59 residues processed: 260 average time/residue: 0.3040 time to fit residues: 134.6848 Evaluate side-chains 263 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 204 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 272 CYS Chi-restraints excluded: chain H residue 282 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 0.7980 chunk 322 optimal weight: 20.0000 chunk 197 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 338 optimal weight: 40.0000 chunk 311 optimal weight: 20.0000 chunk 269 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26160 Z= 0.168 Angle : 0.610 11.436 35608 Z= 0.286 Chirality : 0.042 0.214 4084 Planarity : 0.004 0.048 4600 Dihedral : 6.440 130.697 3792 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.54 % Allowed : 14.00 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 2904 helix: -0.27 (0.16), residues: 1064 sheet: -0.46 (0.21), residues: 496 loop : -0.72 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 86 HIS 0.005 0.001 HIS G 88 PHE 0.042 0.002 PHE E 124 TYR 0.030 0.001 TYR F 169 ARG 0.007 0.000 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8718 (mmm) cc_final: 0.8406 (mmm) REVERT: A 283 MET cc_start: 0.8690 (mmp) cc_final: 0.8311 (mmm) REVERT: B 47 MET cc_start: 0.4931 (tpp) cc_final: 0.4386 (tpt) REVERT: B 123 MET cc_start: 0.8473 (tpp) cc_final: 0.8253 (tpp) REVERT: B 316 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 132 MET cc_start: 0.8602 (ppp) cc_final: 0.8285 (ppp) REVERT: D 305 MET cc_start: 0.8252 (mmm) cc_final: 0.8037 (mmt) REVERT: E 355 MET cc_start: 0.8025 (mtp) cc_final: 0.7718 (mtt) REVERT: F 272 CYS cc_start: 0.6545 (m) cc_final: 0.6275 (m) REVERT: G 82 MET cc_start: 0.8827 (mmm) cc_final: 0.8087 (tmm) REVERT: G 283 MET cc_start: 0.8559 (mmp) cc_final: 0.8247 (mmp) outliers start: 38 outliers final: 35 residues processed: 260 average time/residue: 0.2963 time to fit residues: 133.5179 Evaluate side-chains 253 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 218 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain G residue 292 ASP Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 272 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.0270 chunk 287 optimal weight: 0.3980 chunk 82 optimal weight: 0.0980 chunk 248 optimal weight: 0.0070 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 277 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS F 92 ASN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.101723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080356 restraints weight = 56797.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.082512 restraints weight = 30561.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.083984 restraints weight = 19326.849| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 26160 Z= 0.140 Angle : 0.580 11.127 35608 Z= 0.267 Chirality : 0.041 0.189 4084 Planarity : 0.004 0.049 4600 Dihedral : 5.692 107.517 3792 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.09 % Allowed : 14.77 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2904 helix: 0.08 (0.16), residues: 1056 sheet: 0.00 (0.20), residues: 528 loop : -0.42 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 86 HIS 0.004 0.001 HIS G 371 PHE 0.040 0.001 PHE F 124 TYR 0.021 0.001 TYR F 169 ARG 0.001 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4325.85 seconds wall clock time: 80 minutes 1.38 seconds (4801.38 seconds total)