Starting phenix.real_space_refine on Fri May 16 11:04:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbl_27289/05_2025/8dbl_27289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbl_27289/05_2025/8dbl_27289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbl_27289/05_2025/8dbl_27289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbl_27289/05_2025/8dbl_27289.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbl_27289/05_2025/8dbl_27289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbl_27289/05_2025/8dbl_27289.cif" } resolution = 2.4 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= 0.334 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 24 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 8922 2.51 5 N 2490 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14358 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 318 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 306 not shown) Time building chain proxies: 8.32, per 1000 atoms: 0.58 Number of scatterers: 14358 At special positions: 0 Unit cell: (122.728, 130.134, 77.234, 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 102 16.00 P 24 15.00 Mg 12 11.99 O 2808 8.00 N 2490 7.00 C 8922 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 - 3.00 Amino acid : True - 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: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 43.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.667A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 removed outlier: 3.525A pdb=" N PHE D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 277 through 283 removed outlier: 3.667A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 removed outlier: 3.526A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'F' and resid 12 through 23 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.524A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 277 through 283 removed outlier: 3.666A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER A 169 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 249 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 244 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL A 270 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA A 246 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR A 272 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 248 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER B 169 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 249 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 244 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL B 270 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA B 246 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 272 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B 248 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER C 169 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C 249 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 244 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL C 270 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 246 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR C 272 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU C 248 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER D 169 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 249 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL D 244 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL D 270 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA D 246 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR D 272 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU D 248 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.156A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 3.776A pdb=" N SER E 169 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 249 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL E 244 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL E 270 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA E 246 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N THR E 272 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU E 248 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.157A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 3.775A pdb=" N SER F 169 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR F 249 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL F 244 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL F 270 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 246 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR F 272 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU F 248 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1800 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: 4.35 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4775 1.34 - 1.46: 2118 1.46 - 1.57: 7471 1.57 - 1.69: 24 1.69 - 1.81: 150 Bond restraints: 14538 Sorted by residual: bond pdb=" C1 PRP B 401 " pdb=" O4 PRP B 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP A 401 " pdb=" O4 PRP A 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP C 401 " pdb=" O4 PRP C 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP F 401 " pdb=" O4 PRP F 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1 PRP D 401 " pdb=" O4 PRP D 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 ... (remaining 14533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 19102 1.95 - 3.91: 465 3.91 - 5.86: 89 5.86 - 7.81: 30 7.81 - 9.76: 12 Bond angle restraints: 19698 Sorted by residual: angle pdb=" C THR E 272 " pdb=" CA THR E 272 " pdb=" CB THR E 272 " ideal model delta sigma weight residual 109.51 117.38 -7.87 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR C 272 " pdb=" CA THR C 272 " pdb=" CB THR C 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR A 272 " pdb=" CA THR A 272 " pdb=" CB THR A 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR B 272 " pdb=" CA THR B 272 " pdb=" CB THR B 272 " ideal model delta sigma weight residual 109.51 117.36 -7.85 1.71e+00 3.42e-01 2.11e+01 angle pdb=" C THR F 272 " pdb=" CA THR F 272 " pdb=" CB THR F 272 " ideal model delta sigma weight residual 109.51 117.34 -7.83 1.71e+00 3.42e-01 2.10e+01 ... (remaining 19693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 8013 17.71 - 35.41: 660 35.41 - 53.12: 207 53.12 - 70.82: 60 70.82 - 88.53: 36 Dihedral angle restraints: 8976 sinusoidal: 3600 harmonic: 5376 Sorted by residual: dihedral pdb=" CA GLU C 62 " pdb=" C GLU C 62 " pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU E 62 " pdb=" C GLU E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU B 62 " pdb=" C GLU B 62 " pdb=" N ILE B 63 " pdb=" CA ILE B 63 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1333 0.041 - 0.082: 659 0.082 - 0.124: 267 0.124 - 0.165: 45 0.165 - 0.206: 30 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CA THR D 272 " pdb=" N THR D 272 " pdb=" C THR D 272 " pdb=" CB THR D 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR E 272 " pdb=" N THR E 272 " pdb=" C THR E 272 " pdb=" CB THR E 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR F 272 " pdb=" N THR F 272 " pdb=" C THR F 272 " pdb=" CB THR F 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2331 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 221 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" CG ASP E 221 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 221 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 221 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" CG ASP C 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP C 221 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP C 221 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 221 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" CG ASP F 221 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP F 221 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 221 " -0.015 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 108 2.49 - 3.09: 10320 3.09 - 3.69: 22423 3.69 - 4.30: 34207 4.30 - 4.90: 55860 Nonbonded interactions: 122918 Sorted by model distance: nonbonded pdb=" O3B PRP E 401 " pdb="MG MG E 403 " model vdw 1.885 2.170 nonbonded pdb=" O3B PRP C 401 " pdb="MG MG C 403 " model vdw 1.886 2.170 nonbonded pdb=" O1B PRP F 401 " pdb="MG MG F 403 " model vdw 1.886 2.170 nonbonded pdb=" O3B PRP A 401 " pdb="MG MG A 403 " model vdw 1.886 2.170 nonbonded pdb=" O1B PRP D 401 " pdb="MG MG D 403 " model vdw 1.886 2.170 ... (remaining 122913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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=0.01 max=1.00 mean=0.91 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: 0.860 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.140 Process input model: 32.250 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.011 0.236 14538 Z= 0.534 Angle : 0.823 9.765 19698 Z= 0.454 Chirality : 0.057 0.206 2334 Planarity : 0.003 0.024 2496 Dihedral : 16.538 88.531 5472 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.67 % Allowed : 15.27 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1830 helix: 1.25 (0.20), residues: 738 sheet: -0.62 (0.24), residues: 522 loop : -0.54 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 162 HIS 0.003 0.001 HIS E 193 PHE 0.017 0.002 PHE E 138 TYR 0.027 0.004 TYR B 245 ARG 0.004 0.001 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.15501 ( 648) hydrogen bonds : angle 5.67944 ( 1800) covalent geometry : bond 0.01102 (14538) covalent geometry : angle 0.82307 (19698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 322 time to evaluate : 1.785 Fit side-chains REVERT: A 5 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8431 (mmpt) REVERT: A 115 MET cc_start: 0.8598 (mtp) cc_final: 0.8244 (mtp) REVERT: A 127 MET cc_start: 0.8545 (ttm) cc_final: 0.8273 (ttm) REVERT: A 220 ASP cc_start: 0.8493 (t0) cc_final: 0.8267 (t70) REVERT: A 222 MET cc_start: 0.7806 (ptp) cc_final: 0.7530 (ptp) REVERT: A 267 GLU cc_start: 0.7586 (tp30) cc_final: 0.7162 (tp30) REVERT: B 122 ASP cc_start: 0.8460 (m-30) cc_final: 0.8248 (m-30) REVERT: B 220 ASP cc_start: 0.8601 (t0) cc_final: 0.8173 (t0) REVERT: C 38 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7382 (mp-120) REVERT: C 122 ASP cc_start: 0.8624 (m-30) cc_final: 0.8372 (m-30) REVERT: C 220 ASP cc_start: 0.8648 (t0) cc_final: 0.8328 (t70) REVERT: D 38 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7383 (mp-120) REVERT: D 220 ASP cc_start: 0.8649 (t0) cc_final: 0.8391 (t70) REVERT: E 5 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8457 (mmpt) REVERT: E 122 ASP cc_start: 0.8447 (m-30) cc_final: 0.8239 (m-30) REVERT: E 220 ASP cc_start: 0.8597 (t0) cc_final: 0.8164 (t0) REVERT: F 5 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8429 (mmpt) REVERT: F 115 MET cc_start: 0.8588 (mtp) cc_final: 0.8224 (mtp) REVERT: F 127 MET cc_start: 0.8570 (ttm) cc_final: 0.8294 (ttm) REVERT: F 220 ASP cc_start: 0.8510 (t0) cc_final: 0.8270 (t70) REVERT: F 267 GLU cc_start: 0.7575 (tp30) cc_final: 0.7133 (tp30) outliers start: 42 outliers final: 26 residues processed: 353 average time/residue: 1.2973 time to fit residues: 499.9885 Evaluate side-chains 315 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 285 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 HIS B 288 GLN C 277 GLN C 288 GLN D 277 GLN D 288 GLN E 288 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.159519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.121255 restraints weight = 13614.888| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.43 r_work: 0.3213 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14538 Z= 0.137 Angle : 0.499 4.173 19698 Z= 0.277 Chirality : 0.048 0.174 2334 Planarity : 0.003 0.021 2496 Dihedral : 8.728 70.597 2166 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.77 % Allowed : 12.72 % Favored : 82.51 % 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 (0.21), residues: 1830 helix: 1.75 (0.20), residues: 714 sheet: -0.38 (0.24), residues: 486 loop : 0.02 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 162 HIS 0.003 0.001 HIS B 283 PHE 0.010 0.001 PHE D 138 TYR 0.016 0.002 TYR D 311 ARG 0.002 0.000 ARG D 243 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 648) hydrogen bonds : angle 4.86881 ( 1800) covalent geometry : bond 0.00304 (14538) covalent geometry : angle 0.49903 (19698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 320 time to evaluate : 1.605 Fit side-chains REVERT: A 5 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8648 (mmpt) REVERT: A 17 GLN cc_start: 0.9147 (tp40) cc_final: 0.8840 (tp40) REVERT: A 68 MET cc_start: 0.8716 (tpp) cc_final: 0.8509 (mmm) REVERT: A 96 ARG cc_start: 0.8791 (mtm180) cc_final: 0.8551 (mtm180) REVERT: A 97 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: A 127 MET cc_start: 0.9047 (ttm) cc_final: 0.8795 (ttm) REVERT: A 178 VAL cc_start: 0.8250 (m) cc_final: 0.7852 (t) REVERT: A 180 SER cc_start: 0.8335 (t) cc_final: 0.8056 (t) REVERT: A 220 ASP cc_start: 0.8614 (t0) cc_final: 0.8383 (t70) REVERT: A 222 MET cc_start: 0.8276 (ptp) cc_final: 0.7665 (ptp) REVERT: A 311 TYR cc_start: 0.8579 (t80) cc_final: 0.8341 (t80) REVERT: B 17 GLN cc_start: 0.9083 (tp40) cc_final: 0.8880 (tp-100) REVERT: B 97 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7970 (mm110) REVERT: B 122 ASP cc_start: 0.8808 (m-30) cc_final: 0.8482 (m-30) REVERT: B 220 ASP cc_start: 0.8694 (t0) cc_final: 0.8171 (t0) REVERT: C 17 GLN cc_start: 0.9065 (tp40) cc_final: 0.8700 (tp40) REVERT: C 22 ARG cc_start: 0.8739 (mtp85) cc_final: 0.8531 (mtp85) REVERT: C 68 MET cc_start: 0.8571 (tpp) cc_final: 0.8273 (tpt) REVERT: C 79 ILE cc_start: 0.9184 (pt) cc_final: 0.8883 (mm) REVERT: C 122 ASP cc_start: 0.9014 (m-30) cc_final: 0.8692 (m-30) REVERT: C 220 ASP cc_start: 0.8739 (t0) cc_final: 0.8401 (t70) REVERT: C 282 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8138 (mtpp) REVERT: D 17 GLN cc_start: 0.9099 (tp40) cc_final: 0.8704 (tp40) REVERT: D 68 MET cc_start: 0.8559 (tpp) cc_final: 0.8258 (tpt) REVERT: D 79 ILE cc_start: 0.9196 (pt) cc_final: 0.8877 (mm) REVERT: D 158 ASN cc_start: 0.7561 (m-40) cc_final: 0.7250 (m-40) REVERT: D 220 ASP cc_start: 0.8736 (t0) cc_final: 0.8408 (t70) REVERT: D 282 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8247 (mtpp) REVERT: E 5 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8701 (mmpt) REVERT: E 17 GLN cc_start: 0.9100 (tp40) cc_final: 0.8887 (tp-100) REVERT: E 97 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7960 (mm110) REVERT: E 122 ASP cc_start: 0.8807 (m-30) cc_final: 0.8510 (m-30) REVERT: E 220 ASP cc_start: 0.8696 (t0) cc_final: 0.8179 (t0) REVERT: F 5 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8684 (mmpt) REVERT: F 68 MET cc_start: 0.8737 (tpp) cc_final: 0.8531 (mmm) REVERT: F 79 ILE cc_start: 0.9141 (pt) cc_final: 0.8938 (mm) REVERT: F 97 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: F 127 MET cc_start: 0.9037 (ttm) cc_final: 0.8776 (ttm) REVERT: F 180 SER cc_start: 0.8230 (t) cc_final: 0.8004 (t) REVERT: F 220 ASP cc_start: 0.8624 (t0) cc_final: 0.8389 (t70) REVERT: F 222 MET cc_start: 0.8199 (ptp) cc_final: 0.7799 (ptp) REVERT: F 278 GLU cc_start: 0.7661 (mp0) cc_final: 0.7352 (pm20) REVERT: F 311 TYR cc_start: 0.8671 (t80) cc_final: 0.8466 (t80) outliers start: 75 outliers final: 24 residues processed: 368 average time/residue: 1.2374 time to fit residues: 497.7486 Evaluate side-chains 331 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 298 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 86 optimal weight: 0.0980 chunk 113 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 283 HIS B 97 GLN B 283 HIS C 37 ASN C 283 HIS D 37 ASN E 97 GLN E 283 HIS F 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104377 restraints weight = 13715.671| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.47 r_work: 0.3004 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14538 Z= 0.123 Angle : 0.474 4.185 19698 Z= 0.261 Chirality : 0.047 0.165 2334 Planarity : 0.003 0.022 2496 Dihedral : 6.983 51.882 2148 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.05 % Allowed : 14.69 % Favored : 82.25 % 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: 0.94 (0.20), residues: 1830 helix: 1.94 (0.20), residues: 714 sheet: -0.15 (0.26), residues: 414 loop : -0.17 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.003 0.001 HIS D 12 PHE 0.010 0.001 PHE E 138 TYR 0.017 0.002 TYR E 311 ARG 0.002 0.000 ARG D 22 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 648) hydrogen bonds : angle 4.61836 ( 1800) covalent geometry : bond 0.00272 (14538) covalent geometry : angle 0.47447 (19698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 1.465 Fit side-chains REVERT: A 5 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8609 (mmpt) REVERT: A 17 GLN cc_start: 0.9111 (tp40) cc_final: 0.8831 (tp40) REVERT: A 97 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: A 178 VAL cc_start: 0.8231 (m) cc_final: 0.7865 (t) REVERT: A 180 SER cc_start: 0.8213 (t) cc_final: 0.7960 (t) REVERT: A 220 ASP cc_start: 0.8646 (t0) cc_final: 0.8349 (t70) REVERT: A 222 MET cc_start: 0.8290 (ptp) cc_final: 0.7619 (ptp) REVERT: A 259 SER cc_start: 0.8407 (p) cc_final: 0.8189 (p) REVERT: A 282 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7947 (tttm) REVERT: A 311 TYR cc_start: 0.8575 (t80) cc_final: 0.8320 (t80) REVERT: B 22 ARG cc_start: 0.8798 (mtp85) cc_final: 0.8478 (mtp85) REVERT: B 122 ASP cc_start: 0.8920 (m-30) cc_final: 0.8579 (m-30) REVERT: B 127 MET cc_start: 0.9088 (ttm) cc_final: 0.8873 (tpp) REVERT: B 220 ASP cc_start: 0.8714 (t0) cc_final: 0.8217 (t0) REVERT: B 282 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8228 (mtpp) REVERT: C 17 GLN cc_start: 0.9050 (tp40) cc_final: 0.8758 (tp40) REVERT: C 29 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8716 (mtpt) REVERT: C 68 MET cc_start: 0.8736 (tpp) cc_final: 0.8353 (tpt) REVERT: C 79 ILE cc_start: 0.9105 (pt) cc_final: 0.8882 (mm) REVERT: C 122 ASP cc_start: 0.9089 (m-30) cc_final: 0.8777 (m-30) REVERT: C 158 ASN cc_start: 0.7403 (m-40) cc_final: 0.7009 (m110) REVERT: C 220 ASP cc_start: 0.8770 (t0) cc_final: 0.8376 (t70) REVERT: C 222 MET cc_start: 0.8326 (ptp) cc_final: 0.7941 (ptm) REVERT: C 281 MET cc_start: 0.8598 (mtp) cc_final: 0.8282 (mtp) REVERT: C 282 LYS cc_start: 0.8456 (mtpp) cc_final: 0.8214 (mtpp) REVERT: D 17 GLN cc_start: 0.9070 (tp40) cc_final: 0.8703 (tp40) REVERT: D 29 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8709 (mtpt) REVERT: D 68 MET cc_start: 0.8734 (tpp) cc_final: 0.8345 (tpt) REVERT: D 79 ILE cc_start: 0.9112 (pt) cc_final: 0.8886 (mm) REVERT: D 158 ASN cc_start: 0.7384 (m-40) cc_final: 0.7098 (m-40) REVERT: D 220 ASP cc_start: 0.8765 (t0) cc_final: 0.8365 (t70) REVERT: D 222 MET cc_start: 0.8323 (ptp) cc_final: 0.7935 (ptm) REVERT: D 282 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8194 (mtpp) REVERT: E 5 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8635 (mmpt) REVERT: E 22 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8483 (mtp85) REVERT: E 122 ASP cc_start: 0.8922 (m-30) cc_final: 0.8602 (m-30) REVERT: E 127 MET cc_start: 0.9096 (ttm) cc_final: 0.8886 (tpp) REVERT: E 220 ASP cc_start: 0.8684 (t0) cc_final: 0.8193 (t0) REVERT: E 282 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8170 (mtpp) REVERT: F 5 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8635 (mmpt) REVERT: F 97 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: F 222 MET cc_start: 0.8198 (ptp) cc_final: 0.7917 (ptp) REVERT: F 259 SER cc_start: 0.8333 (p) cc_final: 0.8126 (p) REVERT: F 311 TYR cc_start: 0.8615 (t80) cc_final: 0.8398 (t80) outliers start: 48 outliers final: 19 residues processed: 341 average time/residue: 1.2538 time to fit residues: 467.1578 Evaluate side-chains 323 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 296 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 70 optimal weight: 0.0030 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 89 optimal weight: 0.0770 chunk 162 optimal weight: 7.9990 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 17 GLN B 283 HIS B 288 GLN C 37 ASN C 283 HIS D 37 ASN D 283 HIS E 17 GLN E 283 HIS E 288 GLN F 37 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106145 restraints weight = 13768.845| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.46 r_work: 0.3035 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14538 Z= 0.098 Angle : 0.442 4.262 19698 Z= 0.244 Chirality : 0.046 0.163 2334 Planarity : 0.002 0.023 2496 Dihedral : 6.491 44.977 2142 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.05 % Allowed : 15.90 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1830 helix: 2.04 (0.20), residues: 714 sheet: -0.09 (0.26), residues: 408 loop : -0.28 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 162 HIS 0.002 0.001 HIS E 193 PHE 0.009 0.001 PHE C 138 TYR 0.020 0.001 TYR E 311 ARG 0.001 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 648) hydrogen bonds : angle 4.47852 ( 1800) covalent geometry : bond 0.00215 (14538) covalent geometry : angle 0.44235 (19698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 307 time to evaluate : 1.584 Fit side-chains REVERT: A 17 GLN cc_start: 0.9079 (tp40) cc_final: 0.8796 (tp40) REVERT: A 97 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: A 178 VAL cc_start: 0.8301 (m) cc_final: 0.7943 (t) REVERT: A 222 MET cc_start: 0.8294 (ptp) cc_final: 0.7792 (ptp) REVERT: A 278 GLU cc_start: 0.7737 (mp0) cc_final: 0.7432 (pm20) REVERT: A 311 TYR cc_start: 0.8517 (t80) cc_final: 0.8282 (t80) REVERT: B 22 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8395 (mtp85) REVERT: B 35 PHE cc_start: 0.8133 (m-80) cc_final: 0.7777 (m-80) REVERT: B 97 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7980 (mm110) REVERT: B 115 MET cc_start: 0.9182 (mtp) cc_final: 0.8948 (mtp) REVERT: B 122 ASP cc_start: 0.8930 (m-30) cc_final: 0.8574 (m-30) REVERT: B 220 ASP cc_start: 0.8748 (t0) cc_final: 0.8245 (t0) REVERT: B 282 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8218 (mtpp) REVERT: C 17 GLN cc_start: 0.9060 (tp40) cc_final: 0.8722 (tp40) REVERT: C 22 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8486 (mtp85) REVERT: C 29 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8700 (mtpt) REVERT: C 68 MET cc_start: 0.8722 (tpp) cc_final: 0.8323 (tpt) REVERT: C 122 ASP cc_start: 0.9080 (m-30) cc_final: 0.8765 (m-30) REVERT: C 220 ASP cc_start: 0.8787 (t0) cc_final: 0.8466 (t70) REVERT: C 222 MET cc_start: 0.8322 (ptp) cc_final: 0.8032 (ptm) REVERT: C 282 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8218 (mtpp) REVERT: D 17 GLN cc_start: 0.9061 (tp40) cc_final: 0.8738 (tp40) REVERT: D 29 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8706 (mtpt) REVERT: D 68 MET cc_start: 0.8714 (tpp) cc_final: 0.8310 (tpt) REVERT: D 158 ASN cc_start: 0.7392 (m-40) cc_final: 0.7113 (m-40) REVERT: D 220 ASP cc_start: 0.8775 (t0) cc_final: 0.8454 (t70) REVERT: D 222 MET cc_start: 0.8335 (ptp) cc_final: 0.8057 (ptm) REVERT: D 282 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8174 (mtpp) REVERT: E 22 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8415 (mtp85) REVERT: E 62 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7656 (mm-30) REVERT: E 97 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7997 (mm110) REVERT: E 115 MET cc_start: 0.9178 (mtp) cc_final: 0.8949 (mtp) REVERT: E 122 ASP cc_start: 0.8923 (m-30) cc_final: 0.8588 (m-30) REVERT: E 191 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6572 (mt) REVERT: E 220 ASP cc_start: 0.8709 (t0) cc_final: 0.8217 (t0) REVERT: F 97 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: F 222 MET cc_start: 0.8257 (ptp) cc_final: 0.7873 (ptp) REVERT: F 278 GLU cc_start: 0.7612 (mp0) cc_final: 0.7143 (pm20) outliers start: 48 outliers final: 18 residues processed: 333 average time/residue: 1.2744 time to fit residues: 463.5347 Evaluate side-chains 327 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 157 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 170 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 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 37 ASN A 97 GLN A 283 HIS B 263 ASN B 283 HIS B 288 GLN C 283 HIS D 37 ASN D 283 HIS E 283 HIS E 288 GLN F 37 ASN F 97 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.103588 restraints weight = 14025.743| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.46 r_work: 0.2994 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14538 Z= 0.128 Angle : 0.474 4.325 19698 Z= 0.260 Chirality : 0.047 0.165 2334 Planarity : 0.003 0.022 2496 Dihedral : 6.080 45.159 2130 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.05 % Allowed : 15.90 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1830 helix: 2.07 (0.20), residues: 714 sheet: -0.12 (0.26), residues: 408 loop : -0.25 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 162 HIS 0.003 0.001 HIS C 193 PHE 0.010 0.001 PHE E 138 TYR 0.016 0.002 TYR E 311 ARG 0.006 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 648) hydrogen bonds : angle 4.46042 ( 1800) covalent geometry : bond 0.00292 (14538) covalent geometry : angle 0.47446 (19698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 299 time to evaluate : 2.098 Fit side-chains REVERT: A 17 GLN cc_start: 0.9101 (tp40) cc_final: 0.8762 (tp40) REVERT: A 97 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: A 178 VAL cc_start: 0.8269 (m) cc_final: 0.7901 (t) REVERT: A 222 MET cc_start: 0.8407 (ptp) cc_final: 0.7820 (ptp) REVERT: A 278 GLU cc_start: 0.7748 (mp0) cc_final: 0.7381 (pm20) REVERT: A 311 TYR cc_start: 0.8619 (t80) cc_final: 0.8345 (t80) REVERT: B 35 PHE cc_start: 0.8162 (m-80) cc_final: 0.7834 (m-80) REVERT: B 97 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8098 (mm110) REVERT: B 122 ASP cc_start: 0.8966 (m-30) cc_final: 0.8612 (m-30) REVERT: B 191 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7097 (mt) REVERT: B 220 ASP cc_start: 0.8803 (t0) cc_final: 0.8294 (t0) REVERT: B 282 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8238 (mtpp) REVERT: C 17 GLN cc_start: 0.9070 (tp40) cc_final: 0.8691 (tp40) REVERT: C 29 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8709 (mtpt) REVERT: C 68 MET cc_start: 0.8797 (tpp) cc_final: 0.8360 (tpt) REVERT: C 122 ASP cc_start: 0.9118 (m-30) cc_final: 0.8817 (m-30) REVERT: C 220 ASP cc_start: 0.8838 (t0) cc_final: 0.8509 (t70) REVERT: C 222 MET cc_start: 0.8445 (ptp) cc_final: 0.8123 (ptm) REVERT: C 282 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8235 (mtpp) REVERT: D 17 GLN cc_start: 0.9096 (tp40) cc_final: 0.8745 (tp40) REVERT: D 29 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8725 (mtpt) REVERT: D 68 MET cc_start: 0.8790 (tpp) cc_final: 0.8350 (tpt) REVERT: D 122 ASP cc_start: 0.9068 (m-30) cc_final: 0.8865 (m-30) REVERT: D 220 ASP cc_start: 0.8829 (t0) cc_final: 0.8501 (t70) REVERT: D 222 MET cc_start: 0.8452 (ptp) cc_final: 0.8140 (ptm) REVERT: D 282 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8221 (mtpp) REVERT: E 62 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7819 (mm-30) REVERT: E 97 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8094 (mm110) REVERT: E 122 ASP cc_start: 0.8951 (m-30) cc_final: 0.8657 (m-30) REVERT: E 191 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7080 (mt) REVERT: E 220 ASP cc_start: 0.8806 (t0) cc_final: 0.8336 (t0) REVERT: F 37 ASN cc_start: 0.8845 (p0) cc_final: 0.8643 (p0) REVERT: F 97 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: F 278 GLU cc_start: 0.7644 (mp0) cc_final: 0.7160 (pm20) outliers start: 48 outliers final: 21 residues processed: 335 average time/residue: 1.2882 time to fit residues: 471.6190 Evaluate side-chains 321 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 283 HIS B 283 HIS B 288 GLN C 37 ASN C 283 HIS D 283 HIS E 283 HIS E 288 GLN F 97 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.101940 restraints weight = 13930.353| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.49 r_work: 0.2969 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14538 Z= 0.161 Angle : 0.504 4.389 19698 Z= 0.276 Chirality : 0.048 0.166 2334 Planarity : 0.003 0.025 2496 Dihedral : 6.187 55.757 2130 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.69 % Allowed : 15.08 % Favored : 81.23 % 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: 0.96 (0.20), residues: 1830 helix: 2.03 (0.20), residues: 714 sheet: -0.15 (0.26), residues: 408 loop : -0.24 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 162 HIS 0.003 0.001 HIS C 193 PHE 0.012 0.002 PHE C 138 TYR 0.019 0.002 TYR E 311 ARG 0.005 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 648) hydrogen bonds : angle 4.51271 ( 1800) covalent geometry : bond 0.00371 (14538) covalent geometry : angle 0.50423 (19698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 1.708 Fit side-chains REVERT: A 17 GLN cc_start: 0.9120 (tp40) cc_final: 0.8805 (tp40) REVERT: A 178 VAL cc_start: 0.8199 (m) cc_final: 0.7846 (t) REVERT: A 222 MET cc_start: 0.8386 (ptp) cc_final: 0.7779 (ptp) REVERT: A 278 GLU cc_start: 0.7751 (mp0) cc_final: 0.7343 (pm20) REVERT: A 311 TYR cc_start: 0.8709 (t80) cc_final: 0.8399 (t80) REVERT: B 97 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8111 (mm110) REVERT: B 122 ASP cc_start: 0.8968 (m-30) cc_final: 0.8659 (m-30) REVERT: B 191 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7123 (mt) REVERT: B 220 ASP cc_start: 0.8824 (t0) cc_final: 0.8279 (t0) REVERT: B 282 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8211 (mtpp) REVERT: C 17 GLN cc_start: 0.9052 (tp40) cc_final: 0.8739 (tp40) REVERT: C 29 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8678 (mtpt) REVERT: C 68 MET cc_start: 0.8812 (tpp) cc_final: 0.8382 (tpt) REVERT: C 122 ASP cc_start: 0.9132 (m-30) cc_final: 0.8850 (m-30) REVERT: C 208 VAL cc_start: 0.4926 (OUTLIER) cc_final: 0.4664 (m) REVERT: C 220 ASP cc_start: 0.8824 (t0) cc_final: 0.8371 (t70) REVERT: C 222 MET cc_start: 0.8463 (ptp) cc_final: 0.8002 (ptm) REVERT: C 282 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8250 (mtpp) REVERT: C 314 SER cc_start: 0.6822 (OUTLIER) cc_final: 0.6349 (p) REVERT: D 17 GLN cc_start: 0.9084 (tp40) cc_final: 0.8721 (tp40) REVERT: D 29 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8692 (mtpt) REVERT: D 68 MET cc_start: 0.8800 (tpp) cc_final: 0.8368 (tpt) REVERT: D 158 ASN cc_start: 0.7430 (m-40) cc_final: 0.7147 (m-40) REVERT: D 220 ASP cc_start: 0.8847 (t0) cc_final: 0.8502 (t70) REVERT: D 282 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (mtpp) REVERT: D 314 SER cc_start: 0.6784 (OUTLIER) cc_final: 0.6335 (p) REVERT: E 62 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7775 (mm-30) REVERT: E 97 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8111 (mm110) REVERT: E 122 ASP cc_start: 0.8944 (m-30) cc_final: 0.8650 (m-30) REVERT: E 191 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7135 (mt) REVERT: E 220 ASP cc_start: 0.8817 (t0) cc_final: 0.8291 (t0) REVERT: F 278 GLU cc_start: 0.7638 (mp0) cc_final: 0.7189 (pm20) outliers start: 58 outliers final: 25 residues processed: 339 average time/residue: 1.2504 time to fit residues: 464.3480 Evaluate side-chains 329 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 263 ASN B 283 HIS C 37 ASN C 283 HIS D 283 HIS E 283 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.103691 restraints weight = 13941.995| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.49 r_work: 0.2995 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14538 Z= 0.123 Angle : 0.467 4.368 19698 Z= 0.258 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.023 2496 Dihedral : 6.035 56.161 2130 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.50 % Allowed : 14.89 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1830 helix: 2.04 (0.20), residues: 714 sheet: -0.19 (0.26), residues: 408 loop : -0.27 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.003 0.001 HIS D 193 PHE 0.011 0.001 PHE C 138 TYR 0.023 0.002 TYR C 311 ARG 0.005 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 648) hydrogen bonds : angle 4.41750 ( 1800) covalent geometry : bond 0.00279 (14538) covalent geometry : angle 0.46746 (19698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 296 time to evaluate : 1.501 Fit side-chains REVERT: A 17 GLN cc_start: 0.9090 (tp40) cc_final: 0.8783 (tp40) REVERT: A 97 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: A 178 VAL cc_start: 0.8286 (m) cc_final: 0.7933 (t) REVERT: A 222 MET cc_start: 0.8393 (ptp) cc_final: 0.7767 (ptp) REVERT: A 278 GLU cc_start: 0.7721 (mp0) cc_final: 0.7280 (pm20) REVERT: A 311 TYR cc_start: 0.8648 (t80) cc_final: 0.8409 (t80) REVERT: B 97 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8079 (mm110) REVERT: B 115 MET cc_start: 0.9200 (mtp) cc_final: 0.8939 (mtp) REVERT: B 122 ASP cc_start: 0.8967 (m-30) cc_final: 0.8657 (m-30) REVERT: B 127 MET cc_start: 0.9064 (ttm) cc_final: 0.8847 (tpp) REVERT: B 191 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7135 (mt) REVERT: B 220 ASP cc_start: 0.8790 (t0) cc_final: 0.8267 (t0) REVERT: B 282 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8244 (mtpp) REVERT: C 17 GLN cc_start: 0.9061 (tp40) cc_final: 0.8760 (tp40) REVERT: C 29 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8687 (mtpt) REVERT: C 68 MET cc_start: 0.8767 (tpp) cc_final: 0.8328 (tpt) REVERT: C 191 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6821 (mt) REVERT: C 220 ASP cc_start: 0.8830 (t0) cc_final: 0.8385 (t70) REVERT: C 222 MET cc_start: 0.8339 (ptp) cc_final: 0.7896 (ptm) REVERT: C 282 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: C 314 SER cc_start: 0.6724 (OUTLIER) cc_final: 0.6253 (p) REVERT: D 5 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8347 (mmpt) REVERT: D 17 GLN cc_start: 0.9075 (tp40) cc_final: 0.8722 (tp40) REVERT: D 29 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8689 (mtpt) REVERT: D 68 MET cc_start: 0.8763 (tpp) cc_final: 0.8321 (tpt) REVERT: D 220 ASP cc_start: 0.8822 (t0) cc_final: 0.8477 (t70) REVERT: D 222 MET cc_start: 0.8272 (ptp) cc_final: 0.7986 (ptm) REVERT: D 278 GLU cc_start: 0.7512 (mp0) cc_final: 0.7280 (mp0) REVERT: D 282 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8173 (mtpp) REVERT: D 314 SER cc_start: 0.6670 (OUTLIER) cc_final: 0.6219 (p) REVERT: E 62 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7748 (mm-30) REVERT: E 97 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8020 (mm110) REVERT: E 115 MET cc_start: 0.9200 (mtp) cc_final: 0.8941 (mtp) REVERT: E 122 ASP cc_start: 0.8969 (m-30) cc_final: 0.8674 (m-30) REVERT: E 127 MET cc_start: 0.9070 (ttm) cc_final: 0.8852 (tpp) REVERT: E 191 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7072 (mt) REVERT: E 205 MET cc_start: 0.5330 (ptp) cc_final: 0.4899 (ptm) REVERT: E 220 ASP cc_start: 0.8799 (t0) cc_final: 0.8287 (t0) REVERT: F 22 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8434 (mtp85) REVERT: F 97 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: F 278 GLU cc_start: 0.7580 (mp0) cc_final: 0.7131 (pm20) outliers start: 55 outliers final: 27 residues processed: 337 average time/residue: 1.2273 time to fit residues: 453.2825 Evaluate side-chains 324 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 111 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 159 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 283 HIS E 283 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104898 restraints weight = 14044.223| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.47 r_work: 0.3012 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14538 Z= 0.109 Angle : 0.453 4.379 19698 Z= 0.250 Chirality : 0.046 0.164 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.788 51.393 2129 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.99 % Allowed : 15.52 % Favored : 81.49 % 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: 0.97 (0.20), residues: 1830 helix: 2.08 (0.20), residues: 714 sheet: -0.20 (0.26), residues: 408 loop : -0.25 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 162 HIS 0.003 0.001 HIS D 193 PHE 0.010 0.001 PHE C 138 TYR 0.023 0.002 TYR B 311 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 648) hydrogen bonds : angle 4.33923 ( 1800) covalent geometry : bond 0.00247 (14538) covalent geometry : angle 0.45258 (19698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 1.503 Fit side-chains REVERT: A 17 GLN cc_start: 0.9098 (tp40) cc_final: 0.8807 (tp40) REVERT: A 97 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: A 178 VAL cc_start: 0.8297 (m) cc_final: 0.7943 (t) REVERT: A 222 MET cc_start: 0.8373 (ptp) cc_final: 0.7773 (ptp) REVERT: A 278 GLU cc_start: 0.7729 (mp0) cc_final: 0.7295 (pm20) REVERT: A 311 TYR cc_start: 0.8594 (t80) cc_final: 0.8361 (t80) REVERT: B 97 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8036 (mm110) REVERT: B 122 ASP cc_start: 0.8951 (m-30) cc_final: 0.8612 (m-30) REVERT: B 191 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7146 (mt) REVERT: B 205 MET cc_start: 0.5328 (ptp) cc_final: 0.4872 (ptm) REVERT: B 220 ASP cc_start: 0.8794 (t0) cc_final: 0.8278 (t0) REVERT: B 282 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8247 (mtpp) REVERT: C 17 GLN cc_start: 0.9073 (tp40) cc_final: 0.8732 (tp40) REVERT: C 29 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8690 (mtpt) REVERT: C 68 MET cc_start: 0.8812 (tpp) cc_final: 0.8394 (tpt) REVERT: C 191 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6905 (mt) REVERT: C 208 VAL cc_start: 0.4671 (OUTLIER) cc_final: 0.4394 (m) REVERT: C 220 ASP cc_start: 0.8823 (t0) cc_final: 0.8520 (t70) REVERT: C 222 MET cc_start: 0.8361 (ptp) cc_final: 0.8037 (ptm) REVERT: C 282 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8210 (mtpp) REVERT: D 5 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8337 (mmpt) REVERT: D 17 GLN cc_start: 0.9099 (tp40) cc_final: 0.8750 (tp40) REVERT: D 68 MET cc_start: 0.8805 (tpp) cc_final: 0.8381 (tpt) REVERT: D 220 ASP cc_start: 0.8817 (t0) cc_final: 0.8490 (t70) REVERT: D 222 MET cc_start: 0.8303 (ptp) cc_final: 0.7994 (ptm) REVERT: D 278 GLU cc_start: 0.7535 (mp0) cc_final: 0.7295 (mp0) REVERT: D 282 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: D 314 SER cc_start: 0.6684 (OUTLIER) cc_final: 0.6249 (p) REVERT: E 97 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8047 (mm110) REVERT: E 122 ASP cc_start: 0.8946 (m-30) cc_final: 0.8646 (m-30) REVERT: E 191 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7045 (mt) REVERT: E 205 MET cc_start: 0.5319 (ptp) cc_final: 0.4990 (ptm) REVERT: E 220 ASP cc_start: 0.8791 (t0) cc_final: 0.8303 (t0) REVERT: F 96 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8448 (mtm180) REVERT: F 97 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: F 278 GLU cc_start: 0.7575 (mp0) cc_final: 0.7125 (pm20) outliers start: 47 outliers final: 25 residues processed: 330 average time/residue: 1.3190 time to fit residues: 475.7050 Evaluate side-chains 327 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 LYS Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 97 GLN B 263 ASN B 283 HIS B 288 GLN E 283 HIS E 288 GLN F 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101854 restraints weight = 13724.468| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.48 r_work: 0.2964 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14538 Z= 0.169 Angle : 0.514 4.443 19698 Z= 0.282 Chirality : 0.048 0.164 2334 Planarity : 0.003 0.023 2496 Dihedral : 5.987 56.316 2129 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.12 % Allowed : 15.78 % Favored : 81.11 % 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 (0.20), residues: 1830 helix: 1.98 (0.20), residues: 714 sheet: -0.22 (0.26), residues: 408 loop : -0.24 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 154 HIS 0.004 0.001 HIS C 193 PHE 0.013 0.002 PHE E 138 TYR 0.020 0.002 TYR E 311 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 648) hydrogen bonds : angle 4.46594 ( 1800) covalent geometry : bond 0.00392 (14538) covalent geometry : angle 0.51397 (19698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 1.542 Fit side-chains REVERT: A 17 GLN cc_start: 0.9111 (tp40) cc_final: 0.8794 (tp40) REVERT: A 97 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: A 122 ASP cc_start: 0.9032 (m-30) cc_final: 0.8811 (m-30) REVERT: A 178 VAL cc_start: 0.8215 (m) cc_final: 0.7855 (t) REVERT: A 222 MET cc_start: 0.8442 (ptp) cc_final: 0.7847 (ptp) REVERT: A 278 GLU cc_start: 0.7736 (mp0) cc_final: 0.7263 (pm20) REVERT: A 311 TYR cc_start: 0.8708 (t80) cc_final: 0.8394 (t80) REVERT: B 22 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8642 (mtp85) REVERT: B 122 ASP cc_start: 0.8950 (m-30) cc_final: 0.8652 (m-30) REVERT: B 191 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7196 (mt) REVERT: B 220 ASP cc_start: 0.8829 (t0) cc_final: 0.8295 (t0) REVERT: B 282 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8244 (mtpp) REVERT: C 17 GLN cc_start: 0.9070 (tp40) cc_final: 0.8756 (tp40) REVERT: C 29 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8629 (mtpt) REVERT: C 68 MET cc_start: 0.8817 (tpp) cc_final: 0.8373 (tpt) REVERT: C 122 ASP cc_start: 0.9132 (m-30) cc_final: 0.8786 (m-30) REVERT: C 191 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6925 (mt) REVERT: C 220 ASP cc_start: 0.8824 (t0) cc_final: 0.8359 (t70) REVERT: C 222 MET cc_start: 0.8420 (ptp) cc_final: 0.7924 (ptm) REVERT: C 282 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8231 (mtpp) REVERT: C 314 SER cc_start: 0.6728 (OUTLIER) cc_final: 0.6263 (p) REVERT: D 5 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8363 (mmpt) REVERT: D 17 GLN cc_start: 0.9050 (tp40) cc_final: 0.8803 (tp40) REVERT: D 68 MET cc_start: 0.8795 (tpp) cc_final: 0.8406 (tpt) REVERT: D 220 ASP cc_start: 0.8818 (t0) cc_final: 0.8499 (t70) REVERT: D 278 GLU cc_start: 0.7558 (mp0) cc_final: 0.7311 (mp0) REVERT: D 282 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8196 (mtpp) REVERT: D 314 SER cc_start: 0.6704 (OUTLIER) cc_final: 0.6255 (p) REVERT: E 22 ARG cc_start: 0.8860 (mtp85) cc_final: 0.8635 (mtp85) REVERT: E 62 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7810 (mm-30) REVERT: E 97 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8105 (mm110) REVERT: E 122 ASP cc_start: 0.8961 (m-30) cc_final: 0.8687 (m-30) REVERT: E 191 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7096 (mt) REVERT: E 220 ASP cc_start: 0.8825 (t0) cc_final: 0.8312 (t0) REVERT: F 38 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7833 (mp-120) REVERT: F 97 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: F 278 GLU cc_start: 0.7606 (mp0) cc_final: 0.7138 (pm20) outliers start: 49 outliers final: 25 residues processed: 323 average time/residue: 1.2736 time to fit residues: 449.8136 Evaluate side-chains 315 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 283 HIS E 283 HIS F 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101730 restraints weight = 13813.875| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.48 r_work: 0.2965 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14538 Z= 0.172 Angle : 0.521 4.457 19698 Z= 0.286 Chirality : 0.048 0.167 2334 Planarity : 0.003 0.022 2496 Dihedral : 6.030 59.335 2129 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.80 % Allowed : 16.22 % Favored : 80.98 % 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: 0.84 (0.20), residues: 1830 helix: 1.93 (0.20), residues: 714 sheet: -0.27 (0.26), residues: 408 loop : -0.26 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 162 HIS 0.004 0.001 HIS D 193 PHE 0.012 0.002 PHE E 138 TYR 0.027 0.003 TYR D 311 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 648) hydrogen bonds : angle 4.50045 ( 1800) covalent geometry : bond 0.00399 (14538) covalent geometry : angle 0.52121 (19698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 1.558 Fit side-chains REVERT: A 17 GLN cc_start: 0.9112 (tp40) cc_final: 0.8793 (tp40) REVERT: A 97 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: A 122 ASP cc_start: 0.9031 (m-30) cc_final: 0.8806 (m-30) REVERT: A 178 VAL cc_start: 0.8217 (m) cc_final: 0.7854 (t) REVERT: A 222 MET cc_start: 0.8322 (ptp) cc_final: 0.7721 (ptp) REVERT: A 278 GLU cc_start: 0.7731 (mp0) cc_final: 0.7353 (pm20) REVERT: A 311 TYR cc_start: 0.8707 (t80) cc_final: 0.8395 (t80) REVERT: B 22 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8653 (mtp85) REVERT: B 122 ASP cc_start: 0.8958 (m-30) cc_final: 0.8658 (m-30) REVERT: B 127 MET cc_start: 0.9093 (ttm) cc_final: 0.8783 (tpp) REVERT: B 191 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7220 (mt) REVERT: B 205 MET cc_start: 0.5667 (ptp) cc_final: 0.5206 (ptm) REVERT: B 220 ASP cc_start: 0.8844 (t0) cc_final: 0.8330 (t0) REVERT: B 282 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8244 (mtpp) REVERT: C 17 GLN cc_start: 0.9084 (tp40) cc_final: 0.8782 (tp40) REVERT: C 29 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8638 (mtpt) REVERT: C 68 MET cc_start: 0.8807 (tpp) cc_final: 0.8375 (tpt) REVERT: C 158 ASN cc_start: 0.7446 (m-40) cc_final: 0.7166 (m-40) REVERT: C 220 ASP cc_start: 0.8827 (t0) cc_final: 0.8361 (t70) REVERT: C 222 MET cc_start: 0.8416 (ptp) cc_final: 0.7917 (ptm) REVERT: C 282 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: C 314 SER cc_start: 0.6712 (OUTLIER) cc_final: 0.6247 (p) REVERT: D 5 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8374 (mmpt) REVERT: D 17 GLN cc_start: 0.9029 (tp40) cc_final: 0.8771 (tp40) REVERT: D 68 MET cc_start: 0.8797 (tpp) cc_final: 0.8369 (tpt) REVERT: D 158 ASN cc_start: 0.7417 (m-40) cc_final: 0.7133 (m-40) REVERT: D 282 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8198 (mtpp) REVERT: D 314 SER cc_start: 0.6683 (OUTLIER) cc_final: 0.6224 (p) REVERT: E 22 ARG cc_start: 0.8861 (mtp85) cc_final: 0.8631 (mtp85) REVERT: E 62 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7846 (mm-30) REVERT: E 97 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8036 (mm110) REVERT: E 122 ASP cc_start: 0.8957 (m-30) cc_final: 0.8681 (m-30) REVERT: E 127 MET cc_start: 0.9100 (ttm) cc_final: 0.8788 (tpp) REVERT: E 191 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7160 (mt) REVERT: E 205 MET cc_start: 0.5724 (ptp) cc_final: 0.5204 (ptm) REVERT: E 220 ASP cc_start: 0.8836 (t0) cc_final: 0.8344 (t0) REVERT: F 97 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: F 278 GLU cc_start: 0.7597 (mp0) cc_final: 0.7130 (pm20) outliers start: 44 outliers final: 29 residues processed: 310 average time/residue: 1.3627 time to fit residues: 461.0593 Evaluate side-chains 321 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 114 optimal weight: 0.0870 chunk 161 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 283 HIS E 283 HIS F 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104664 restraints weight = 13884.509| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.48 r_work: 0.3003 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14538 Z= 0.109 Angle : 0.459 4.394 19698 Z= 0.254 Chirality : 0.046 0.166 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.773 57.489 2129 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.61 % Allowed : 16.48 % Favored : 80.92 % 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: 0.88 (0.20), residues: 1830 helix: 1.99 (0.20), residues: 714 sheet: -0.23 (0.26), residues: 408 loop : -0.29 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.002 0.001 HIS D 193 PHE 0.010 0.001 PHE B 138 TYR 0.026 0.002 TYR D 311 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 648) hydrogen bonds : angle 4.35622 ( 1800) covalent geometry : bond 0.00246 (14538) covalent geometry : angle 0.45866 (19698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12287.75 seconds wall clock time: 211 minutes 42.06 seconds (12702.06 seconds total)