Starting phenix.real_space_refine (version: dev) on Sat Feb 25 15:22:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/02_2023/7ztc_14957_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/02_2023/7ztc_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_14957/02_2023/7ztc_14957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/02_2023/7ztc_14957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/02_2023/7ztc_14957_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ztc_14957/02_2023/7ztc_14957_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 14.16, per 1000 atoms: 0.55 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: 10.30 Conformation dependent library (CDL) restraints added in 3.4 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: 2.77 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: 9.04 Time building geometry restraints manager: 11.11 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 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. 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: 2.760 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: 16.270 Check model and map are aligned: 0.380 Process input model: 64.830 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 % 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 *********************** 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 : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.3869 time to fit residues: 368.1464 Evaluate side-chains 277 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0494 ------------------------------------------------------------------------------- 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: 5.9990 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 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 G 88 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: 0.8262 moved from start: 0.2783 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= 0.195 Angle : 0.639 8.934 35608 Z= 0.309 Chirality : 0.044 0.205 4084 Planarity : 0.004 0.039 4600 Dihedral : 9.727 152.334 3792 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 2904 helix: -0.71 (0.15), residues: 1056 sheet: -0.01 (0.23), residues: 496 loop : -0.00 (0.18), residues: 1352 *********************** 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 381 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 326 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 28 residues processed: 368 average time/residue: 0.3252 time to fit residues: 196.7486 Evaluate side-chains 280 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 2.712 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2181 time to fit residues: 15.1438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 309 optimal weight: 30.0000 chunk 334 optimal weight: 30.0000 chunk 275 optimal weight: 5.9990 chunk 306 optimal weight: 40.0000 chunk 105 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS D 49 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN F 49 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 26160 Z= 0.351 Angle : 0.696 8.746 35608 Z= 0.341 Chirality : 0.047 0.223 4084 Planarity : 0.005 0.052 4600 Dihedral : 9.298 142.508 3792 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 2904 helix: -0.68 (0.15), residues: 1056 sheet: -0.12 (0.22), residues: 496 loop : -0.27 (0.17), residues: 1352 *********************** 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 300 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 25 residues processed: 289 average time/residue: 0.3119 time to fit residues: 151.4723 Evaluate side-chains 234 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 2.877 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2191 time to fit residues: 14.0284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 160 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 147 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 310 optimal weight: 40.0000 chunk 328 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 294 optimal weight: 20.0000 chunk 88 optimal weight: 0.0020 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 353 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3851 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= 0.170 Angle : 0.581 7.509 35608 Z= 0.275 Chirality : 0.042 0.188 4084 Planarity : 0.004 0.051 4600 Dihedral : 8.460 150.821 3792 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2904 helix: -0.26 (0.15), residues: 1056 sheet: -0.17 (0.21), residues: 496 loop : -0.18 (0.17), residues: 1352 *********************** 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 286 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 256 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 271 average time/residue: 0.3351 time to fit residues: 153.0892 Evaluate side-chains 237 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 222 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2476 time to fit residues: 10.8801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 4.9990 chunk 186 optimal weight: 0.0970 chunk 4 optimal weight: 0.0030 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 294 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 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: 0.8372 moved from start: 0.4133 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= 0.198 Angle : 0.594 7.953 35608 Z= 0.281 Chirality : 0.043 0.215 4084 Planarity : 0.004 0.051 4600 Dihedral : 7.975 179.841 3792 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2904 helix: -0.22 (0.16), residues: 1056 sheet: -0.19 (0.20), residues: 496 loop : -0.29 (0.17), residues: 1352 *********************** 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 263 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 259 average time/residue: 0.3267 time to fit residues: 143.7795 Evaluate side-chains 223 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 215 time to evaluate : 3.064 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2344 time to fit residues: 7.4607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 0.9990 chunk 295 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 192 optimal weight: 0.0980 chunk 81 optimal weight: 6.9990 chunk 328 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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** ** 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 26160 Z= 0.242 Angle : 0.623 10.182 35608 Z= 0.295 Chirality : 0.044 0.212 4084 Planarity : 0.004 0.051 4600 Dihedral : 7.699 178.195 3792 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 2904 helix: -0.27 (0.16), residues: 1056 sheet: -0.21 (0.20), residues: 496 loop : -0.44 (0.17), residues: 1352 *********************** 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 261 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 243 average time/residue: 0.3213 time to fit residues: 133.3077 Evaluate side-chains 231 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2351 time to fit residues: 13.1471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 187 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 327 optimal weight: 30.0000 chunk 205 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 26160 Z= 0.288 Angle : 0.650 11.349 35608 Z= 0.311 Chirality : 0.045 0.222 4084 Planarity : 0.005 0.051 4600 Dihedral : 7.491 174.969 3792 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 2904 helix: -0.37 (0.16), residues: 1056 sheet: -0.35 (0.21), residues: 496 loop : -0.61 (0.17), residues: 1352 *********************** 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 232 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 3.007 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 226 average time/residue: 0.3229 time to fit residues: 124.4298 Evaluate side-chains 211 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 200 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2255 time to fit residues: 8.4326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 98 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4629 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= 0.202 Angle : 0.605 11.327 35608 Z= 0.284 Chirality : 0.043 0.193 4084 Planarity : 0.004 0.050 4600 Dihedral : 6.809 140.163 3792 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 2904 helix: -0.23 (0.16), residues: 1056 sheet: -0.29 (0.21), residues: 496 loop : -0.56 (0.17), residues: 1352 *********************** 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 231 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 224 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 229 average time/residue: 0.3300 time to fit residues: 129.1647 Evaluate side-chains 209 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 2.973 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2389 time to fit residues: 5.2342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 305 optimal weight: 40.0000 chunk 183 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 288 optimal weight: 30.0000 chunk 304 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** B 314 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 26160 Z= 0.364 Angle : 0.704 13.692 35608 Z= 0.338 Chirality : 0.047 0.254 4084 Planarity : 0.005 0.050 4600 Dihedral : 7.080 138.550 3792 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 2904 helix: -0.35 (0.16), residues: 1016 sheet: -0.43 (0.21), residues: 496 loop : -0.79 (0.16), residues: 1392 *********************** 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 220 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 2.937 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 215 average time/residue: 0.3235 time to fit residues: 118.4603 Evaluate side-chains 207 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2428 time to fit residues: 7.0159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 0.8980 chunk 322 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 338 optimal weight: 40.0000 chunk 311 optimal weight: 20.0000 chunk 269 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 208 optimal weight: 0.0270 chunk 165 optimal weight: 0.6980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 161 HIS ** A 275 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** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 26160 Z= 0.165 Angle : 0.593 12.026 35608 Z= 0.276 Chirality : 0.042 0.201 4084 Planarity : 0.004 0.049 4600 Dihedral : 6.306 126.155 3792 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 2904 helix: -0.21 (0.16), residues: 1064 sheet: -0.32 (0.21), residues: 496 loop : -0.56 (0.17), residues: 1344 ********************** 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 235 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.3261 time to fit residues: 130.9474 Evaluate side-chains 217 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 2.782 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 0.0050 chunk 277 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 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** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 HIS ** H 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.076447 restraints weight = 57842.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.078518 restraints weight = 31529.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.079949 restraints weight = 20209.220| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 26160 Z= 0.182 Angle : 0.598 11.616 35608 Z= 0.278 Chirality : 0.043 0.207 4084 Planarity : 0.004 0.050 4600 Dihedral : 6.070 114.736 3792 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.20 % 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: -0.58 (0.15), residues: 2904 helix: -0.09 (0.16), residues: 1056 sheet: -0.21 (0.21), residues: 496 loop : -0.56 (0.17), residues: 1352 =============================================================================== Job complete usr+sys time: 4070.07 seconds wall clock time: 76 minutes 22.08 seconds (4582.08 seconds total)