Starting phenix.real_space_refine on Fri Mar 15 13:46:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/03_2024/6djm_7936_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/03_2024/6djm_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_7936/03_2024/6djm_7936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/03_2024/6djm_7936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/03_2024/6djm_7936_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djm_7936/03_2024/6djm_7936_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.47, per 1000 atoms: 0.55 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: 4.25 Conformation dependent library (CDL) restraints added in 2.2 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: 2.20 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: 3.42 Time building geometry restraints manager: 4.66 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: 7184 30.13 - 60.26: 108 60.26 - 90.38: 8 90.38 - 120.51: 0 120.51 - 150.64: 4 Dihedral angle restraints: 7304 sinusoidal: 3004 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 7301 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 7.580 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 33.340 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 11.490 150.638 4552 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 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP A 340 HIS 0.011 0.003 HIS A 40 PHE 0.024 0.003 PHE A 124 TYR 0.012 0.002 TYR A 218 ARG 0.007 0.001 ARG C 335 *********************** 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 : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8090 (m-30) cc_final: 0.7878 (m-30) REVERT: B 227 MET cc_start: 0.8515 (mmm) cc_final: 0.8275 (mmm) REVERT: C 44 MET cc_start: 0.8306 (mmt) cc_final: 0.8038 (mmm) REVERT: C 305 MET cc_start: 0.8099 (mmm) cc_final: 0.7838 (mmt) REVERT: D 24 ASP cc_start: 0.7452 (m-30) cc_final: 0.7206 (m-30) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2972 time to fit residues: 119.9492 Evaluate side-chains 143 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 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 A 225 ASN B 161 HIS B 162 ASN B 173 HIS C 49 GLN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12020 Z= 0.192 Angle : 0.551 7.496 16320 Z= 0.283 Chirality : 0.044 0.133 1808 Planarity : 0.005 0.044 2084 Dihedral : 10.343 162.728 1756 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.96 % Allowed : 8.20 % Favored : 90.84 % 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: -2.76 (0.20), residues: 1468 helix: -2.84 (0.16), residues: 584 sheet: -1.43 (0.31), residues: 236 loop : -0.71 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS C 40 PHE 0.008 0.001 PHE D 262 TYR 0.010 0.001 TYR A 53 ARG 0.006 0.001 ARG A 206 *********************** 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 : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8440 (mmt) cc_final: 0.8109 (mmt) REVERT: B 47 MET cc_start: 0.7041 (ppp) cc_final: 0.6720 (ppp) REVERT: B 80 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: C 44 MET cc_start: 0.8234 (mmt) cc_final: 0.7936 (mmm) REVERT: D 47 MET cc_start: 0.7491 (ppp) cc_final: 0.7254 (ppp) outliers start: 12 outliers final: 6 residues processed: 169 average time/residue: 0.2063 time to fit residues: 52.7035 Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 80 ASP 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: 3.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 12020 Z= 0.488 Angle : 0.663 6.532 16320 Z= 0.337 Chirality : 0.050 0.147 1808 Planarity : 0.005 0.040 2084 Dihedral : 10.370 172.349 1756 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.31 % Allowed : 8.44 % Favored : 89.25 % 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: -2.13 (0.21), residues: 1468 helix: -2.17 (0.18), residues: 608 sheet: -0.99 (0.34), residues: 236 loop : -0.48 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 340 HIS 0.012 0.002 HIS C 40 PHE 0.011 0.002 PHE C 223 TYR 0.016 0.002 TYR A 143 ARG 0.007 0.001 ARG C 147 *********************** 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 155 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8150 (tp40) cc_final: 0.7948 (mm-40) REVERT: B 47 MET cc_start: 0.7124 (ppp) cc_final: 0.6787 (ppp) REVERT: B 305 MET cc_start: 0.7924 (mmt) cc_final: 0.7455 (mmt) REVERT: C 242 LEU cc_start: 0.8537 (mp) cc_final: 0.8282 (mt) REVERT: C 325 MET cc_start: 0.7162 (mmp) cc_final: 0.6916 (mmt) REVERT: D 47 MET cc_start: 0.7537 (ppp) cc_final: 0.6909 (ppp) outliers start: 29 outliers final: 18 residues processed: 149 average time/residue: 0.2028 time to fit residues: 46.1417 Evaluate side-chains 135 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 135 optimal weight: 0.2980 chunk 143 optimal weight: 0.6980 chunk 70 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 225 ASN B 115 ASN B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12020 Z= 0.160 Angle : 0.496 6.479 16320 Z= 0.252 Chirality : 0.043 0.135 1808 Planarity : 0.004 0.037 2084 Dihedral : 9.970 175.229 1756 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.07 % Allowed : 9.63 % Favored : 88.30 % 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: -1.45 (0.22), residues: 1468 helix: -1.48 (0.21), residues: 592 sheet: -0.81 (0.34), residues: 236 loop : -0.23 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 340 HIS 0.003 0.001 HIS B 40 PHE 0.006 0.001 PHE B 31 TYR 0.009 0.001 TYR A 169 ARG 0.004 0.001 ARG C 147 *********************** 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 156 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8463 (mmt) cc_final: 0.8253 (mmt) REVERT: B 80 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: B 305 MET cc_start: 0.7792 (mmt) cc_final: 0.7365 (mmt) REVERT: C 305 MET cc_start: 0.8100 (mmt) cc_final: 0.7801 (mmt) REVERT: C 325 MET cc_start: 0.7116 (mmp) cc_final: 0.6862 (mmt) REVERT: D 47 MET cc_start: 0.7548 (ppp) cc_final: 0.7278 (ppp) REVERT: D 107 GLU cc_start: 0.7436 (pt0) cc_final: 0.7025 (pt0) outliers start: 26 outliers final: 14 residues processed: 152 average time/residue: 0.1939 time to fit residues: 45.7983 Evaluate side-chains 137 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 233 SER 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: 0.9980 chunk 106 optimal weight: 0.0060 chunk 59 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 0.0040 overall best weight: 0.3808 ------------------------------------------------------------------------------- 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 115 ASN B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12020 Z= 0.140 Angle : 0.477 7.992 16320 Z= 0.239 Chirality : 0.043 0.124 1808 Planarity : 0.003 0.036 2084 Dihedral : 9.806 176.959 1756 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.99 % Allowed : 10.19 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1468 helix: -1.14 (0.21), residues: 596 sheet: -0.63 (0.34), residues: 236 loop : -0.04 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.005 0.001 PHE D 31 TYR 0.007 0.001 TYR A 143 ARG 0.004 0.000 ARG C 147 *********************** 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 150 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.519 Fit side-chains REVERT: B 47 MET cc_start: 0.7179 (ppp) cc_final: 0.6888 (ppp) REVERT: B 80 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: B 305 MET cc_start: 0.7775 (mmt) cc_final: 0.7358 (mmt) REVERT: C 305 MET cc_start: 0.8126 (mmt) cc_final: 0.7818 (mmt) REVERT: C 325 MET cc_start: 0.7096 (mmp) cc_final: 0.6848 (mmt) REVERT: D 47 MET cc_start: 0.7519 (ppp) cc_final: 0.7263 (ppp) REVERT: D 107 GLU cc_start: 0.7472 (pt0) cc_final: 0.7051 (pt0) outliers start: 25 outliers final: 15 residues processed: 147 average time/residue: 0.2011 time to fit residues: 45.6046 Evaluate side-chains 145 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 233 SER 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: 5.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 115 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: 0.8215 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12020 Z= 0.409 Angle : 0.594 7.036 16320 Z= 0.299 Chirality : 0.048 0.133 1808 Planarity : 0.005 0.037 2084 Dihedral : 10.074 178.650 1756 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.23 % Allowed : 10.67 % Favored : 87.10 % 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: -1.24 (0.22), residues: 1468 helix: -1.26 (0.21), residues: 612 sheet: -0.57 (0.35), residues: 236 loop : -0.18 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 79 HIS 0.007 0.002 HIS D 40 PHE 0.009 0.001 PHE C 223 TYR 0.013 0.002 TYR A 143 ARG 0.007 0.001 ARG C 147 *********************** 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 150 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.393 Fit side-chains REVERT: A 41 GLN cc_start: 0.7815 (tp40) cc_final: 0.7473 (pm20) REVERT: A 47 MET cc_start: 0.7130 (ppp) cc_final: 0.6778 (ppp) REVERT: A 246 GLN cc_start: 0.7794 (mt0) cc_final: 0.7362 (mp10) REVERT: B 80 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: B 305 MET cc_start: 0.7876 (mmt) cc_final: 0.7520 (mmt) REVERT: C 47 MET cc_start: 0.6624 (ppp) cc_final: 0.6373 (ppp) REVERT: C 314 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: C 325 MET cc_start: 0.7226 (mmp) cc_final: 0.6970 (mmt) REVERT: D 47 MET cc_start: 0.7497 (ppp) cc_final: 0.7176 (ppp) REVERT: D 107 GLU cc_start: 0.7375 (pt0) cc_final: 0.6913 (pt0) outliers start: 28 outliers final: 20 residues processed: 146 average time/residue: 0.1883 time to fit residues: 42.9780 Evaluate side-chains 144 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.0570 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3269 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= 0.175 Angle : 0.492 6.310 16320 Z= 0.249 Chirality : 0.044 0.124 1808 Planarity : 0.003 0.036 2084 Dihedral : 9.806 173.917 1756 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.75 % Allowed : 11.46 % Favored : 86.78 % 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: -0.94 (0.23), residues: 1468 helix: -0.96 (0.21), residues: 616 sheet: -0.51 (0.35), residues: 236 loop : -0.03 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.003 0.001 HIS A 40 PHE 0.005 0.001 PHE C 223 TYR 0.007 0.001 TYR A 143 ARG 0.006 0.001 ARG A 116 *********************** 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 151 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.743 Fit side-chains REVERT: A 41 GLN cc_start: 0.7735 (tp40) cc_final: 0.7479 (pm20) REVERT: A 47 MET cc_start: 0.7132 (ppp) cc_final: 0.6759 (ppp) REVERT: A 246 GLN cc_start: 0.7753 (mt0) cc_final: 0.7371 (mp10) REVERT: B 80 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: C 47 MET cc_start: 0.6569 (ppp) cc_final: 0.6194 (ppp) REVERT: C 305 MET cc_start: 0.8133 (mmt) cc_final: 0.7784 (mmt) REVERT: C 314 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: C 325 MET cc_start: 0.7255 (mmp) cc_final: 0.6996 (mmt) REVERT: D 47 MET cc_start: 0.7418 (ppp) cc_final: 0.7077 (ppp) REVERT: D 107 GLU cc_start: 0.7395 (pt0) cc_final: 0.6948 (pt0) outliers start: 22 outliers final: 14 residues processed: 148 average time/residue: 0.1967 time to fit residues: 44.8431 Evaluate side-chains 139 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8181 moved from start: 0.3336 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= 0.237 Angle : 0.503 6.871 16320 Z= 0.253 Chirality : 0.044 0.124 1808 Planarity : 0.004 0.036 2084 Dihedral : 9.751 170.747 1756 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.91 % Allowed : 11.31 % Favored : 86.78 % 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: -0.79 (0.23), residues: 1468 helix: -0.86 (0.21), residues: 616 sheet: -0.33 (0.36), residues: 228 loop : 0.04 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 79 HIS 0.004 0.001 HIS A 40 PHE 0.006 0.001 PHE C 223 TYR 0.009 0.001 TYR A 143 ARG 0.007 0.001 ARG C 147 *********************** 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 150 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.551 Fit side-chains REVERT: A 41 GLN cc_start: 0.7815 (tp40) cc_final: 0.7505 (pm20) REVERT: A 47 MET cc_start: 0.7192 (ppp) cc_final: 0.6846 (ppp) REVERT: A 246 GLN cc_start: 0.7793 (mt0) cc_final: 0.7446 (mp-120) REVERT: B 80 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: C 305 MET cc_start: 0.8146 (mmt) cc_final: 0.7805 (mmt) REVERT: C 314 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: D 47 MET cc_start: 0.7366 (ppp) cc_final: 0.6982 (ppp) REVERT: D 107 GLU cc_start: 0.7359 (pt0) cc_final: 0.6908 (pt0) outliers start: 24 outliers final: 17 residues processed: 144 average time/residue: 0.1939 time to fit residues: 43.6400 Evaluate side-chains 141 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 84 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 80 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 B 162 ASN B 225 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12020 Z= 0.164 Angle : 0.480 6.580 16320 Z= 0.242 Chirality : 0.043 0.122 1808 Planarity : 0.003 0.035 2084 Dihedral : 9.636 168.908 1756 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.51 % Allowed : 12.18 % Favored : 86.31 % 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 (0.23), residues: 1468 helix: -0.69 (0.22), residues: 616 sheet: -0.26 (0.36), residues: 228 loop : 0.12 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 79 HIS 0.003 0.001 HIS B 40 PHE 0.006 0.001 PHE B 223 TYR 0.007 0.001 TYR A 143 ARG 0.004 0.000 ARG C 147 *********************** 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 144 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.434 Fit side-chains REVERT: A 41 GLN cc_start: 0.7752 (tp40) cc_final: 0.7527 (pm20) REVERT: A 47 MET cc_start: 0.7211 (ppp) cc_final: 0.6870 (ppp) REVERT: A 246 GLN cc_start: 0.7784 (mt0) cc_final: 0.7419 (mp-120) REVERT: C 47 MET cc_start: 0.6519 (ppp) cc_final: 0.6183 (ppp) REVERT: C 305 MET cc_start: 0.8146 (mmt) cc_final: 0.7809 (mmt) REVERT: C 314 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: D 47 MET cc_start: 0.7373 (ppp) cc_final: 0.6973 (ppp) REVERT: D 107 GLU cc_start: 0.7383 (pt0) cc_final: 0.7071 (pt0) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.1797 time to fit residues: 40.0616 Evaluate side-chains 140 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 233 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 90 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12020 Z= 0.156 Angle : 0.475 7.043 16320 Z= 0.238 Chirality : 0.043 0.122 1808 Planarity : 0.003 0.034 2084 Dihedral : 9.545 167.301 1756 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.35 % Allowed : 12.10 % Favored : 86.54 % 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 (0.23), residues: 1468 helix: -0.56 (0.22), residues: 616 sheet: -0.33 (0.40), residues: 172 loop : 0.03 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.005 0.001 PHE D 31 TYR 0.007 0.001 TYR A 143 ARG 0.003 0.000 ARG A 147 ********************** 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 141 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.441 Fit side-chains REVERT: A 41 GLN cc_start: 0.7760 (tp40) cc_final: 0.7538 (pm20) REVERT: A 47 MET cc_start: 0.7221 (ppp) cc_final: 0.6887 (ppp) REVERT: A 246 GLN cc_start: 0.7773 (mt0) cc_final: 0.7427 (mp-120) REVERT: C 305 MET cc_start: 0.8141 (mmt) cc_final: 0.7801 (mmt) REVERT: C 355 MET cc_start: 0.7760 (mtm) cc_final: 0.7400 (ptp) REVERT: D 47 MET cc_start: 0.7383 (ppp) cc_final: 0.6978 (ppp) REVERT: D 107 GLU cc_start: 0.7403 (pt0) cc_final: 0.7099 (pt0) outliers start: 17 outliers final: 15 residues processed: 139 average time/residue: 0.1912 time to fit residues: 41.7298 Evaluate side-chains 139 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 233 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.102051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.088176 restraints weight = 18144.714| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.90 r_work: 0.3019 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12020 Z= 0.188 Angle : 0.487 8.707 16320 Z= 0.242 Chirality : 0.043 0.120 1808 Planarity : 0.003 0.035 2084 Dihedral : 9.523 166.412 1756 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.19 % Allowed : 12.34 % Favored : 86.46 % 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: -0.51 (0.23), residues: 1468 helix: -0.50 (0.22), residues: 616 sheet: -0.26 (0.40), residues: 172 loop : 0.03 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.005 0.001 PHE D 31 TYR 0.007 0.001 TYR A 143 ARG 0.003 0.000 ARG D 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.39 seconds wall clock time: 45 minutes 54.36 seconds (2754.36 seconds total)