Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:15:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/02_2023/6djm_7936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/02_2023/6djm_7936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/02_2023/6djm_7936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/02_2023/6djm_7936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/02_2023/6djm_7936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/02_2023/6djm_7936_updated.pdb" } resolution = 3.1 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= 0.002 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 ARG 28": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11768 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.22, per 1000 atoms: 0.61 Number of scatterers: 11768 At special positions: 0 Unit cell: (101.365, 78.375, 165.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 2276 8.00 N 1984 7.00 C 7408 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: 5.15 Conformation dependent library (CDL) restraints added in 2.0 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 16 sheets defined 36.0% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 143 removed outlier: 4.065A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.580A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.670A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.865A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 4.063A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 258 - end of helix removed outlier: 4.498A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 261' Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.504A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.843A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 3.608A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.655A pdb=" N ILE A 369 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 143 removed outlier: 4.066A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 192 removed outlier: 3.580A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.670A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 removed outlier: 3.865A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 261 removed outlier: 4.063A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix removed outlier: 4.497A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 261' Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.504A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.842A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.608A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.655A pdb=" N ILE B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 370' Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 143 removed outlier: 4.065A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 192 removed outlier: 3.581A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.670A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.865A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.063A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.497A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 261' Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.504A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.843A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 removed outlier: 3.608A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.655A pdb=" N ILE C 369 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 370' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 143 removed outlier: 4.065A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 192 removed outlier: 3.580A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.670A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.865A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.505A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.842A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.608A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 366 through 370 removed outlier: 3.655A pdb=" N ILE D 369 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 366 through 370' Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.778A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.547A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.414A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) 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: 6.778A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.547A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.414A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) 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: 6.778A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.547A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.415A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) 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: 6.778A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 34 through 38 removed outlier: 3.547A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.414A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 305 hydrogen bonds defined for protein. 825 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: 3.49 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3633 1.33 - 1.45: 1729 1.45 - 1.57: 6494 1.57 - 1.68: 12 1.68 - 1.80: 152 Bond restraints: 12020 Sorted by residual: bond pdb=" O3A ANP C 802 " pdb=" PB ANP C 802 " ideal model delta sigma weight residual 1.700 1.538 0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" O3A ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP B 802 " pdb=" PB ANP B 802 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP D 802 " pdb=" PB ANP D 802 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" O5' ANP C 802 " pdb=" PA ANP C 802 " ideal model delta sigma weight residual 1.655 1.549 0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 12015 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.68: 483 106.68 - 113.52: 6544 113.52 - 120.35: 4723 120.35 - 127.19: 4426 127.19 - 134.03: 144 Bond angle restraints: 16320 Sorted by residual: angle pdb=" PB ANP A 802 " pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 126.95 108.53 18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" PB ANP B 802 " pdb=" N3B ANP B 802 " pdb=" PG ANP B 802 " ideal model delta sigma weight residual 126.95 109.57 17.38 3.00e+00 1.11e-01 3.36e+01 angle pdb=" PB ANP D 802 " pdb=" N3B ANP D 802 " pdb=" PG ANP D 802 " ideal model delta sigma weight residual 126.95 110.79 16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" PB ANP C 802 " pdb=" N3B ANP C 802 " pdb=" PG ANP C 802 " ideal model delta sigma weight residual 126.95 111.66 15.29 3.00e+00 1.11e-01 2.60e+01 angle pdb=" O1B ANP C 802 " pdb=" PB ANP C 802 " pdb=" O2B ANP C 802 " ideal model delta sigma weight residual 120.08 108.34 11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.13: 7090 30.13 - 60.26: 90 60.26 - 90.38: 8 90.38 - 120.51: 0 120.51 - 150.64: 4 Dihedral angle restraints: 7192 sinusoidal: 2892 harmonic: 4300 Sorted by residual: dihedral pdb=" CA TYR A 166 " pdb=" C TYR A 166 " pdb=" N GLU A 167 " pdb=" CA GLU A 167 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR C 166 " pdb=" C TYR C 166 " pdb=" N GLU C 167 " pdb=" CA GLU C 167 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA TYR B 166 " pdb=" C TYR B 166 " pdb=" N GLU B 167 " pdb=" CA GLU B 167 " ideal model delta harmonic sigma weight residual -180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 7189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1284 0.060 - 0.120: 470 0.120 - 0.179: 34 0.179 - 0.239: 17 0.239 - 0.299: 3 Chirality restraints: 1808 Sorted by residual: chirality pdb=" C3' ANP A 802 " pdb=" C2' ANP A 802 " pdb=" C4' ANP A 802 " pdb=" O3' ANP A 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ANP B 802 " pdb=" C2' ANP B 802 " pdb=" C4' ANP B 802 " pdb=" O3' ANP B 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' ANP D 802 " pdb=" C2' ANP D 802 " pdb=" C4' ANP D 802 " pdb=" O3' ANP D 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO B 243 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO D 243 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO C 243 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.033 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 146 2.64 - 3.20: 10047 3.20 - 3.77: 17962 3.77 - 4.33: 26795 4.33 - 4.90: 43200 Nonbonded interactions: 98150 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O2G ANP B 802 " model vdw 2.069 2.170 nonbonded pdb="MG MG A 801 " pdb=" O3G ANP A 802 " model vdw 2.078 2.170 nonbonded pdb="MG MG D 801 " pdb=" O2G ANP D 802 " model vdw 2.078 2.170 nonbonded pdb="MG MG C 801 " pdb=" O2G ANP C 802 " model vdw 2.087 2.170 nonbonded pdb="MG MG C 801 " pdb=" O2B ANP C 802 " model vdw 2.093 2.170 ... (remaining 98145 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' } 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1984 2.21 5 O 2276 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 8.400 Check model and map are aligned: 0.180 Process input model: 34.410 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.010 0.162 12020 Z= 0.652 Angle : 1.005 18.422 16320 Z= 0.505 Chirality : 0.060 0.299 1808 Planarity : 0.007 0.059 2084 Dihedral : 10.989 150.638 4440 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -4.16 (0.18), residues: 1468 helix: -4.37 (0.10), residues: 568 sheet: -1.57 (0.35), residues: 196 loop : -1.50 (0.21), residues: 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2968 time to fit residues: 119.7565 Evaluate side-chains 144 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 161 HIS A 162 ASN A 173 HIS B 161 HIS B 162 ASN B 173 HIS C 161 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN D 49 GLN D 161 HIS D 225 ASN D 353 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 12020 Z= 0.193 Angle : 0.547 7.469 16320 Z= 0.282 Chirality : 0.044 0.134 1808 Planarity : 0.005 0.044 2084 Dihedral : 9.254 156.830 1644 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.96 % 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: -2.75 (0.20), residues: 1468 helix: -2.84 (0.16), residues: 584 sheet: -1.42 (0.31), residues: 236 loop : -0.71 (0.25), residues: 648 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 169 average time/residue: 0.2229 time to fit residues: 56.5867 Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1136 time to fit residues: 3.2198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 115 ASN C 49 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 12020 Z= 0.456 Angle : 0.647 6.513 16320 Z= 0.328 Chirality : 0.049 0.185 1808 Planarity : 0.005 0.041 2084 Dihedral : 9.509 165.587 1644 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 1.67 % 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: -2.09 (0.21), residues: 1468 helix: -2.14 (0.18), residues: 608 sheet: -0.98 (0.34), residues: 236 loop : -0.44 (0.26), residues: 624 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.486 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 142 average time/residue: 0.2177 time to fit residues: 47.0713 Evaluate side-chains 125 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.548 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1177 time to fit residues: 4.2463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 chunk 14 optimal weight: 0.0570 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 115 ASN B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 12020 Z= 0.169 Angle : 0.494 6.456 16320 Z= 0.250 Chirality : 0.043 0.132 1808 Planarity : 0.004 0.037 2084 Dihedral : 9.121 168.987 1644 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.96 % 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: -1.41 (0.22), residues: 1468 helix: -1.46 (0.21), residues: 592 sheet: -0.77 (0.34), residues: 236 loop : -0.20 (0.26), residues: 640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.488 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 133 average time/residue: 0.2007 time to fit residues: 41.8340 Evaluate side-chains 125 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.487 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1652 time to fit residues: 3.5578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 0.0020 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 115 ASN B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 12020 Z= 0.239 Angle : 0.520 7.617 16320 Z= 0.261 Chirality : 0.045 0.131 1808 Planarity : 0.004 0.036 2084 Dihedral : 9.065 173.546 1644 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1468 helix: -1.28 (0.21), residues: 616 sheet: -0.55 (0.35), residues: 236 loop : -0.05 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.483 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 139 average time/residue: 0.2023 time to fit residues: 43.5827 Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1076 time to fit residues: 2.5298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 143 optimal weight: 0.0570 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN C 173 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12020 Z= 0.159 Angle : 0.481 6.777 16320 Z= 0.241 Chirality : 0.043 0.144 1808 Planarity : 0.003 0.036 2084 Dihedral : 8.918 175.361 1644 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1468 helix: -0.95 (0.21), residues: 616 sheet: -0.47 (0.35), residues: 236 loop : 0.02 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.502 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 139 average time/residue: 0.2092 time to fit residues: 44.7645 Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1121 time to fit residues: 2.4045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 115 ASN B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 12020 Z= 0.220 Angle : 0.509 10.129 16320 Z= 0.254 Chirality : 0.044 0.137 1808 Planarity : 0.004 0.036 2084 Dihedral : 8.959 179.496 1644 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1468 helix: -0.83 (0.21), residues: 616 sheet: -0.36 (0.36), residues: 236 loop : 0.04 (0.27), residues: 616 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.500 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 131 average time/residue: 0.2006 time to fit residues: 41.2087 Evaluate side-chains 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 12020 Z= 0.240 Angle : 0.517 12.105 16320 Z= 0.257 Chirality : 0.044 0.131 1808 Planarity : 0.004 0.036 2084 Dihedral : 8.926 176.223 1644 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer Outliers : 0.64 % 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: -0.81 (0.23), residues: 1468 helix: -0.76 (0.22), residues: 616 sheet: -0.52 (0.38), residues: 180 loop : -0.10 (0.25), residues: 672 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.534 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 130 average time/residue: 0.2173 time to fit residues: 45.0924 Evaluate side-chains 126 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1430 time to fit residues: 3.1106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 132 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.0000 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12020 Z= 0.174 Angle : 0.489 13.695 16320 Z= 0.243 Chirality : 0.043 0.131 1808 Planarity : 0.003 0.035 2084 Dihedral : 8.816 176.317 1644 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1468 helix: -0.60 (0.22), residues: 616 sheet: -0.40 (0.39), residues: 180 loop : -0.03 (0.25), residues: 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.549 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2174 time to fit residues: 43.8909 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1199 time to fit residues: 2.3915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 12020 Z= 0.315 Angle : 0.556 13.776 16320 Z= 0.276 Chirality : 0.046 0.143 1808 Planarity : 0.004 0.037 2084 Dihedral : 8.928 172.769 1644 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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: -0.76 (0.23), residues: 1468 helix: -0.68 (0.22), residues: 612 sheet: -0.44 (0.38), residues: 180 loop : -0.14 (0.25), residues: 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.488 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1963 time to fit residues: 38.0585 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.087626 restraints weight = 18264.671| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.88 r_work: 0.3009 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12020 Z= 0.225 Angle : 0.512 12.511 16320 Z= 0.254 Chirality : 0.044 0.123 1808 Planarity : 0.004 0.036 2084 Dihedral : 8.859 172.743 1644 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: -0.58 (0.23), residues: 1468 helix: -0.58 (0.22), residues: 612 sheet: -0.23 (0.36), residues: 236 loop : 0.03 (0.27), residues: 620 =============================================================================== Job complete usr+sys time: 2330.70 seconds wall clock time: 43 minutes 37.83 seconds (2617.83 seconds total)