Starting phenix.real_space_refine on Thu Jun 12 21:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbl_27289/06_2025/8dbl_27289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbl_27289/06_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_27289/06_2025/8dbl_27289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbl_27289/06_2025/8dbl_27289.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbl_27289/06_2025/8dbl_27289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbl_27289/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.81, per 1000 atoms: 0.61 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: 3.82 Conformation dependent library (CDL) restraints added in 1.9 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: 1.46 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: 4.25 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.11 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: 1.280 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: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 33.020 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 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:33.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.390 ------------------------------------------------------------------------------- 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 : 1.580 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: 1.4049 time to fit residues: 539.4280 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 : 1.565 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121325 restraints weight = 13614.888| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.42 r_work: 0.3212 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 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 = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 1.739 Fit side-chains REVERT: A 5 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8648 (mmpt) REVERT: A 17 GLN cc_start: 0.9146 (tp40) cc_final: 0.8839 (tp40) REVERT: A 68 MET cc_start: 0.8716 (tpp) cc_final: 0.8508 (mmm) REVERT: A 96 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8550 (mtm180) REVERT: A 97 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: A 127 MET cc_start: 0.9045 (ttm) cc_final: 0.8793 (ttm) REVERT: A 178 VAL cc_start: 0.8249 (m) cc_final: 0.7850 (t) REVERT: A 180 SER cc_start: 0.8337 (t) cc_final: 0.8059 (t) REVERT: A 220 ASP cc_start: 0.8613 (t0) cc_final: 0.8382 (t70) REVERT: A 222 MET cc_start: 0.8273 (ptp) cc_final: 0.7662 (ptp) REVERT: A 311 TYR cc_start: 0.8579 (t80) cc_final: 0.8341 (t80) REVERT: B 17 GLN cc_start: 0.9081 (tp40) cc_final: 0.8878 (tp-100) REVERT: B 97 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7967 (mm110) REVERT: B 122 ASP cc_start: 0.8806 (m-30) cc_final: 0.8480 (m-30) REVERT: B 220 ASP cc_start: 0.8693 (t0) cc_final: 0.8170 (t0) REVERT: C 17 GLN cc_start: 0.9063 (tp40) cc_final: 0.8698 (tp40) REVERT: C 22 ARG cc_start: 0.8738 (mtp85) cc_final: 0.8530 (mtp85) REVERT: C 68 MET cc_start: 0.8569 (tpp) cc_final: 0.8271 (tpt) REVERT: C 79 ILE cc_start: 0.9184 (pt) cc_final: 0.8883 (mm) REVERT: C 122 ASP cc_start: 0.9013 (m-30) cc_final: 0.8690 (m-30) REVERT: C 220 ASP cc_start: 0.8739 (t0) cc_final: 0.8400 (t70) REVERT: C 282 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8138 (mtpp) REVERT: D 17 GLN cc_start: 0.9097 (tp40) cc_final: 0.8702 (tp40) REVERT: D 68 MET cc_start: 0.8557 (tpp) cc_final: 0.8256 (tpt) REVERT: D 79 ILE cc_start: 0.9196 (pt) cc_final: 0.8877 (mm) REVERT: D 158 ASN cc_start: 0.7560 (m-40) cc_final: 0.7249 (m-40) REVERT: D 220 ASP cc_start: 0.8735 (t0) cc_final: 0.8407 (t70) REVERT: D 282 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8247 (mtpp) REVERT: E 5 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8700 (mmpt) REVERT: E 17 GLN cc_start: 0.9099 (tp40) cc_final: 0.8886 (tp-100) REVERT: E 97 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7958 (mm110) REVERT: E 122 ASP cc_start: 0.8807 (m-30) cc_final: 0.8511 (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: 0.8683 (mmpt) REVERT: F 68 MET cc_start: 0.8736 (tpp) cc_final: 0.8529 (mmm) REVERT: F 79 ILE cc_start: 0.9141 (pt) cc_final: 0.8938 (mm) REVERT: F 97 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: F 127 MET cc_start: 0.9037 (ttm) cc_final: 0.8776 (ttm) REVERT: F 180 SER cc_start: 0.8235 (t) cc_final: 0.8009 (t) REVERT: F 220 ASP cc_start: 0.8623 (t0) cc_final: 0.8387 (t70) REVERT: F 222 MET cc_start: 0.8196 (ptp) cc_final: 0.7796 (ptp) REVERT: F 278 GLU cc_start: 0.7662 (mp0) cc_final: 0.7355 (pm20) REVERT: F 311 TYR cc_start: 0.8670 (t80) cc_final: 0.8466 (t80) outliers start: 75 outliers final: 24 residues processed: 368 average time/residue: 1.3367 time to fit residues: 537.2029 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 : 1.639 ------------------------------------------------------------------------------- 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: 3.9990 chunk 140 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 283 HIS C 37 ASN C 283 HIS D 37 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS F 97 GLN F 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103361 restraints weight = 13709.695| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.47 r_work: 0.2989 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1594 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= 0.137 Angle : 0.491 4.185 19698 Z= 0.270 Chirality : 0.047 0.166 2334 Planarity : 0.003 0.022 2496 Dihedral : 7.033 50.385 2148 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.12 % Allowed : 14.57 % Favored : 82.32 % 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 (0.21), residues: 1830 helix: 1.92 (0.20), residues: 714 sheet: -0.28 (0.25), residues: 486 loop : -0.06 (0.25), residues: 630 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 0.011 0.002 PHE F 138 TYR 0.016 0.002 TYR E 311 ARG 0.002 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 648) hydrogen bonds : angle 4.65487 ( 1800) covalent geometry : bond 0.00306 (14538) covalent geometry : angle 0.49059 (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 357 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 1.503 Fit side-chains REVERT: A 5 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8602 (mmpt) REVERT: A 17 GLN cc_start: 0.9112 (tp40) cc_final: 0.8826 (tp40) REVERT: A 97 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: A 178 VAL cc_start: 0.8260 (m) cc_final: 0.7886 (t) REVERT: A 180 SER cc_start: 0.8224 (t) cc_final: 0.7941 (t) REVERT: A 220 ASP cc_start: 0.8659 (t0) cc_final: 0.8360 (t70) REVERT: A 222 MET cc_start: 0.8289 (ptp) cc_final: 0.7602 (ptp) REVERT: A 259 SER cc_start: 0.8421 (p) cc_final: 0.8178 (p) REVERT: A 282 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7971 (tttm) REVERT: A 311 TYR cc_start: 0.8618 (t80) cc_final: 0.8347 (t80) REVERT: B 22 ARG cc_start: 0.8811 (mtp85) cc_final: 0.8499 (mtp85) REVERT: B 122 ASP cc_start: 0.8928 (m-30) cc_final: 0.8600 (m-30) REVERT: B 127 MET cc_start: 0.9097 (ttm) cc_final: 0.8874 (tpp) REVERT: B 180 SER cc_start: 0.8207 (t) cc_final: 0.8005 (t) REVERT: B 220 ASP cc_start: 0.8733 (t0) cc_final: 0.8239 (t0) REVERT: B 282 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8234 (mtpp) REVERT: C 17 GLN cc_start: 0.9071 (tp40) cc_final: 0.8786 (tp40) REVERT: C 29 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8715 (mtpt) REVERT: C 68 MET cc_start: 0.8735 (tpp) cc_final: 0.8346 (tpt) REVERT: C 79 ILE cc_start: 0.9155 (pt) cc_final: 0.8878 (mm) REVERT: C 122 ASP cc_start: 0.9091 (m-30) cc_final: 0.8768 (m-30) REVERT: C 220 ASP cc_start: 0.8770 (t0) cc_final: 0.8375 (t70) REVERT: C 222 MET cc_start: 0.8355 (ptp) cc_final: 0.7966 (ptm) REVERT: C 281 MET cc_start: 0.8616 (mtp) cc_final: 0.8351 (mtp) REVERT: C 282 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8221 (mtpp) REVERT: D 17 GLN cc_start: 0.9087 (tp40) cc_final: 0.8728 (tp40) REVERT: D 29 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8728 (mtpt) REVERT: D 68 MET cc_start: 0.8739 (tpp) cc_final: 0.8347 (tpt) REVERT: D 79 ILE cc_start: 0.9154 (pt) cc_final: 0.8872 (mm) REVERT: D 158 ASN cc_start: 0.7468 (m-40) cc_final: 0.7177 (m-40) REVERT: D 220 ASP cc_start: 0.8781 (t0) cc_final: 0.8378 (t70) REVERT: D 222 MET cc_start: 0.8340 (ptp) cc_final: 0.7955 (ptm) REVERT: D 282 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8192 (mtpp) REVERT: E 5 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8615 (mmpt) REVERT: E 22 ARG cc_start: 0.8818 (mtp85) cc_final: 0.8605 (mtp85) REVERT: E 62 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7728 (mm-30) REVERT: E 97 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7964 (mm110) REVERT: E 122 ASP cc_start: 0.8931 (m-30) cc_final: 0.8622 (m-30) REVERT: E 127 MET cc_start: 0.9100 (ttm) cc_final: 0.8880 (tpp) REVERT: E 220 ASP cc_start: 0.8700 (t0) cc_final: 0.8211 (t0) REVERT: E 282 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8176 (mtpp) REVERT: F 5 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8607 (mmpt) REVERT: F 97 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: F 259 SER cc_start: 0.8373 (p) cc_final: 0.8142 (p) outliers start: 49 outliers final: 23 residues processed: 337 average time/residue: 1.5784 time to fit residues: 579.7926 Evaluate side-chains 330 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 63 ILE 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 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 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 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 97 GLN 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 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 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: 5.9990 chunk 166 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 263 ASN B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 283 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN E 263 ASN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100620 restraints weight = 13728.302| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.46 r_work: 0.2950 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14538 Z= 0.198 Angle : 0.546 4.670 19698 Z= 0.299 Chirality : 0.049 0.168 2334 Planarity : 0.003 0.023 2496 Dihedral : 6.992 50.671 2142 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.94 % Allowed : 14.31 % Favored : 81.74 % 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: 0.83 (0.20), residues: 1830 helix: 1.84 (0.20), residues: 714 sheet: -0.29 (0.25), residues: 480 loop : -0.11 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.004 0.001 HIS C 193 PHE 0.014 0.002 PHE E 138 TYR 0.016 0.002 TYR A 146 ARG 0.002 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 648) hydrogen bonds : angle 4.70587 ( 1800) covalent geometry : bond 0.00459 (14538) covalent geometry : angle 0.54617 (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 356 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 1.969 Fit side-chains REVERT: A 5 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8599 (mmpt) REVERT: A 17 GLN cc_start: 0.9125 (tp40) cc_final: 0.8792 (tp40) REVERT: A 97 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: A 122 ASP cc_start: 0.9003 (m-30) cc_final: 0.8730 (m-30) REVERT: A 178 VAL cc_start: 0.8265 (m) cc_final: 0.7891 (t) REVERT: A 220 ASP cc_start: 0.8681 (t0) cc_final: 0.8365 (t70) REVERT: A 222 MET cc_start: 0.8307 (ptp) cc_final: 0.7614 (ptp) REVERT: A 259 SER cc_start: 0.8424 (p) cc_final: 0.8212 (p) REVERT: A 278 GLU cc_start: 0.7683 (mp0) cc_final: 0.7323 (pm20) REVERT: B 22 ARG cc_start: 0.8869 (mtp85) cc_final: 0.8568 (mtp85) REVERT: B 97 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8004 (mm110) REVERT: B 122 ASP cc_start: 0.8943 (m-30) cc_final: 0.8666 (m-30) REVERT: B 220 ASP cc_start: 0.8826 (t0) cc_final: 0.8300 (t0) REVERT: B 282 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8212 (mtpp) REVERT: C 17 GLN cc_start: 0.9056 (tp40) cc_final: 0.8793 (tp40) REVERT: C 29 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8641 (mtpt) REVERT: C 38 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7219 (mp-120) REVERT: C 68 MET cc_start: 0.8794 (tpp) cc_final: 0.8389 (tpt) REVERT: C 79 ILE cc_start: 0.9220 (pt) cc_final: 0.8850 (mm) REVERT: C 122 ASP cc_start: 0.9117 (m-30) cc_final: 0.8747 (m-30) REVERT: C 220 ASP cc_start: 0.8775 (t0) cc_final: 0.8357 (t70) REVERT: C 222 MET cc_start: 0.8437 (ptp) cc_final: 0.7988 (ptm) REVERT: C 278 GLU cc_start: 0.7532 (mp0) cc_final: 0.7149 (pm20) REVERT: C 282 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8259 (mtpp) REVERT: C 314 SER cc_start: 0.6758 (OUTLIER) cc_final: 0.6271 (p) REVERT: D 17 GLN cc_start: 0.9055 (tp40) cc_final: 0.8816 (tp40) REVERT: D 29 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8652 (mtpt) REVERT: D 68 MET cc_start: 0.8795 (tpp) cc_final: 0.8389 (tpt) REVERT: D 79 ILE cc_start: 0.9223 (pt) cc_final: 0.8848 (mm) REVERT: D 220 ASP cc_start: 0.8813 (t0) cc_final: 0.8503 (t70) REVERT: D 282 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8257 (mtpp) REVERT: D 314 SER cc_start: 0.6756 (OUTLIER) cc_final: 0.6291 (p) REVERT: E 5 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8560 (mtpt) REVERT: E 22 ARG cc_start: 0.8860 (mtp85) cc_final: 0.8564 (mtp85) REVERT: E 65 ASP cc_start: 0.8689 (m-30) cc_final: 0.8481 (m-30) REVERT: E 97 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7998 (mm110) REVERT: E 122 ASP cc_start: 0.8945 (m-30) cc_final: 0.8687 (m-30) REVERT: E 191 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7082 (mt) REVERT: E 220 ASP cc_start: 0.8796 (t0) cc_final: 0.8296 (t0) REVERT: E 282 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8191 (mtpp) REVERT: F 5 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8609 (mmpt) REVERT: F 96 ARG cc_start: 0.8939 (mtm180) cc_final: 0.8723 (mtm180) REVERT: F 259 SER cc_start: 0.8355 (p) cc_final: 0.8148 (p) REVERT: F 278 GLU cc_start: 0.7731 (mp0) cc_final: 0.7282 (pm20) outliers start: 62 outliers final: 31 residues processed: 334 average time/residue: 1.4371 time to fit residues: 522.5634 Evaluate side-chains 335 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 63 ILE 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 259 SER Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 38 GLN 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 307 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 31 VAL 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 307 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 5 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 E residue 314 SER Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN A 283 HIS B 12 HIS B 283 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 HIS E 12 HIS E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.100767 restraints weight = 13887.303| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.48 r_work: 0.2938 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14538 Z= 0.187 Angle : 0.533 4.455 19698 Z= 0.293 Chirality : 0.049 0.168 2334 Planarity : 0.003 0.022 2496 Dihedral : 6.923 53.948 2142 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.39 % Allowed : 13.17 % Favored : 82.44 % 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: 0.75 (0.20), residues: 1830 helix: 1.79 (0.20), residues: 714 sheet: -0.38 (0.24), residues: 480 loop : -0.14 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 162 HIS 0.004 0.001 HIS C 193 PHE 0.014 0.002 PHE D 138 TYR 0.019 0.002 TYR C 311 ARG 0.002 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 648) hydrogen bonds : angle 4.69239 ( 1800) covalent geometry : bond 0.00431 (14538) covalent geometry : angle 0.53310 (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 362 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 1.624 Fit side-chains REVERT: A 5 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8632 (mmpt) REVERT: A 17 GLN cc_start: 0.9118 (tp40) cc_final: 0.8790 (tp40) REVERT: A 122 ASP cc_start: 0.9051 (m-30) cc_final: 0.8784 (m-30) REVERT: A 178 VAL cc_start: 0.8258 (m) cc_final: 0.7888 (t) REVERT: A 222 MET cc_start: 0.8438 (ptp) cc_final: 0.7945 (ptp) REVERT: A 259 SER cc_start: 0.8421 (p) cc_final: 0.8204 (p) REVERT: A 311 TYR cc_start: 0.8688 (t80) cc_final: 0.8419 (t80) REVERT: B 22 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8565 (mtp85) REVERT: B 62 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 97 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8007 (mm110) REVERT: B 122 ASP cc_start: 0.8959 (m-30) cc_final: 0.8681 (m-30) REVERT: B 191 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7153 (mt) REVERT: B 220 ASP cc_start: 0.8802 (t0) cc_final: 0.8280 (t0) REVERT: B 282 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8211 (mtpp) REVERT: C 17 GLN cc_start: 0.9044 (tp40) cc_final: 0.8806 (tp40) REVERT: C 29 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8651 (mtpt) REVERT: C 38 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7096 (mp-120) REVERT: C 68 MET cc_start: 0.8776 (tpp) cc_final: 0.8382 (tpt) REVERT: C 79 ILE cc_start: 0.9206 (pt) cc_final: 0.8844 (mm) REVERT: C 122 ASP cc_start: 0.9127 (m-30) cc_final: 0.8746 (m-30) REVERT: C 220 ASP cc_start: 0.8775 (t0) cc_final: 0.8352 (t70) REVERT: C 222 MET cc_start: 0.8422 (ptp) cc_final: 0.7977 (ptm) REVERT: C 281 MET cc_start: 0.8621 (mtp) cc_final: 0.8377 (mtp) REVERT: C 282 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8269 (mtpp) REVERT: C 314 SER cc_start: 0.6713 (OUTLIER) cc_final: 0.6230 (p) REVERT: D 17 GLN cc_start: 0.9050 (tp40) cc_final: 0.8811 (tp40) REVERT: D 29 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8658 (mtpt) REVERT: D 68 MET cc_start: 0.8780 (tpp) cc_final: 0.8383 (tpt) REVERT: D 79 ILE cc_start: 0.9215 (pt) cc_final: 0.8848 (mm) REVERT: D 220 ASP cc_start: 0.8808 (t0) cc_final: 0.8499 (t70) REVERT: D 282 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8240 (mtpp) REVERT: D 314 SER cc_start: 0.6704 (OUTLIER) cc_final: 0.6245 (p) REVERT: E 5 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8578 (mtpt) REVERT: E 22 ARG cc_start: 0.8837 (mtp85) cc_final: 0.8564 (mtp85) REVERT: E 97 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7991 (mm110) REVERT: E 122 ASP cc_start: 0.8963 (m-30) cc_final: 0.8703 (m-30) REVERT: E 191 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7074 (mt) REVERT: E 220 ASP cc_start: 0.8790 (t0) cc_final: 0.8260 (t0) REVERT: E 282 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8192 (mtpp) REVERT: F 5 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8591 (mmpt) REVERT: F 96 ARG cc_start: 0.8876 (mtm180) cc_final: 0.8670 (mtm180) REVERT: F 259 SER cc_start: 0.8338 (p) cc_final: 0.8128 (p) outliers start: 69 outliers final: 32 residues processed: 340 average time/residue: 1.4105 time to fit residues: 522.7992 Evaluate side-chains 332 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 314 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 259 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 31 VAL 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 270 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 31 VAL 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 307 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 5 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 E residue 314 SER Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 314 SER 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: 0.9990 chunk 97 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 283 HIS D 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 283 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103246 restraints weight = 14065.019| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.46 r_work: 0.2982 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1907 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 4.334 19698 Z= 0.262 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.023 2496 Dihedral : 6.553 57.193 2142 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.07 % Allowed : 13.68 % 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: 0.85 (0.20), residues: 1830 helix: 1.94 (0.20), residues: 714 sheet: -0.22 (0.26), residues: 408 loop : -0.29 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 162 HIS 0.004 0.001 HIS E 12 PHE 0.012 0.001 PHE E 138 TYR 0.022 0.002 TYR D 311 ARG 0.004 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 648) hydrogen bonds : angle 4.52481 ( 1800) covalent geometry : bond 0.00290 (14538) covalent geometry : angle 0.47424 (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 366 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 1.533 Fit side-chains REVERT: A 17 GLN cc_start: 0.9113 (tp40) cc_final: 0.8822 (tp40) REVERT: A 97 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: A 178 VAL cc_start: 0.8243 (m) cc_final: 0.7887 (t) REVERT: A 180 SER cc_start: 0.8221 (t) cc_final: 0.7999 (t) REVERT: A 222 MET cc_start: 0.8380 (ptp) cc_final: 0.7821 (ptp) REVERT: A 259 SER cc_start: 0.8380 (p) cc_final: 0.8164 (p) REVERT: A 278 GLU cc_start: 0.7685 (mp0) cc_final: 0.7229 (pm20) REVERT: A 311 TYR cc_start: 0.8648 (t80) cc_final: 0.8399 (t80) REVERT: B 22 ARG cc_start: 0.8816 (mtp85) cc_final: 0.8502 (mtp85) REVERT: B 97 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8000 (mm110) REVERT: B 122 ASP cc_start: 0.8966 (m-30) cc_final: 0.8650 (m-30) REVERT: B 127 MET cc_start: 0.9088 (ttm) cc_final: 0.8880 (tpp) REVERT: B 191 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7115 (mt) REVERT: B 220 ASP cc_start: 0.8798 (t0) cc_final: 0.8282 (t0) REVERT: B 282 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8233 (mtpp) REVERT: C 17 GLN cc_start: 0.9098 (tp40) cc_final: 0.8796 (tp40) REVERT: C 29 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8703 (mtpt) REVERT: C 68 MET cc_start: 0.8755 (tpp) cc_final: 0.8345 (tpt) REVERT: C 220 ASP cc_start: 0.8768 (t0) cc_final: 0.8346 (t70) REVERT: C 222 MET cc_start: 0.8414 (ptp) cc_final: 0.7996 (ptm) REVERT: C 278 GLU cc_start: 0.7482 (mp0) cc_final: 0.7082 (pm20) REVERT: C 282 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8263 (mtpp) REVERT: D 5 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8421 (mmpt) REVERT: D 17 GLN cc_start: 0.9102 (tp40) cc_final: 0.8764 (tp40) REVERT: D 29 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8708 (mtpt) REVERT: D 68 MET cc_start: 0.8748 (tpp) cc_final: 0.8338 (tpt) REVERT: D 79 ILE cc_start: 0.9111 (pt) cc_final: 0.8909 (mm) REVERT: D 220 ASP cc_start: 0.8772 (t0) cc_final: 0.8452 (t70) REVERT: D 282 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8243 (mtpp) REVERT: E 22 ARG cc_start: 0.8804 (mtp85) cc_final: 0.8494 (mtp85) REVERT: E 122 ASP cc_start: 0.8967 (m-30) cc_final: 0.8688 (m-30) REVERT: E 127 MET cc_start: 0.9094 (ttm) cc_final: 0.8887 (tpp) REVERT: E 191 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7133 (mt) REVERT: E 220 ASP cc_start: 0.8791 (t0) cc_final: 0.8271 (t0) REVERT: E 282 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8213 (mtpp) REVERT: F 96 ARG cc_start: 0.8860 (mtm180) cc_final: 0.8644 (mtm180) REVERT: F 278 GLU cc_start: 0.7682 (mp0) cc_final: 0.7203 (pm20) outliers start: 64 outliers final: 26 residues processed: 344 average time/residue: 1.2961 time to fit residues: 487.4478 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 : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 128 ASP 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 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 249 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 314 SER 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 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 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 249 THR Chi-restraints excluded: chain E residue 259 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 283 HIS C 283 HIS D 283 HIS ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.102102 restraints weight = 13936.685| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.49 r_work: 0.2961 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14538 Z= 0.149 Angle : 0.496 4.376 19698 Z= 0.274 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.023 2496 Dihedral : 6.161 51.482 2130 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.31 % Allowed : 14.63 % 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: 0.82 (0.20), residues: 1830 helix: 1.89 (0.20), residues: 714 sheet: -0.25 (0.26), residues: 408 loop : -0.28 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 162 HIS 0.003 0.001 HIS C 193 PHE 0.012 0.002 PHE E 138 TYR 0.020 0.002 TYR E 311 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 648) hydrogen bonds : angle 4.51239 ( 1800) covalent geometry : bond 0.00341 (14538) covalent geometry : angle 0.49620 (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 356 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 304 time to evaluate : 1.565 Fit side-chains REVERT: A 17 GLN cc_start: 0.9109 (tp40) cc_final: 0.8802 (tp40) REVERT: A 97 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: A 122 ASP cc_start: 0.9016 (m-30) cc_final: 0.8781 (m-30) REVERT: A 178 VAL cc_start: 0.8239 (m) cc_final: 0.7882 (t) REVERT: A 180 SER cc_start: 0.8205 (t) cc_final: 0.7985 (t) REVERT: A 222 MET cc_start: 0.8483 (ptp) cc_final: 0.7901 (ptp) REVERT: A 259 SER cc_start: 0.8370 (p) cc_final: 0.8159 (p) REVERT: A 278 GLU cc_start: 0.7719 (mp0) cc_final: 0.7296 (pm20) REVERT: A 311 TYR cc_start: 0.8667 (t80) cc_final: 0.8405 (t80) REVERT: B 22 ARG cc_start: 0.8828 (mtp85) cc_final: 0.8475 (mtp85) REVERT: B 97 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8013 (mm110) REVERT: B 122 ASP cc_start: 0.8945 (m-30) cc_final: 0.8644 (m-30) REVERT: B 127 MET cc_start: 0.9111 (ttm) cc_final: 0.8771 (tpp) REVERT: B 191 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7162 (mt) REVERT: B 220 ASP cc_start: 0.8827 (t0) cc_final: 0.8551 (t70) REVERT: B 282 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8242 (mtpp) REVERT: C 17 GLN cc_start: 0.9078 (tp40) cc_final: 0.8736 (tp40) REVERT: C 29 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8708 (mtpt) REVERT: C 68 MET cc_start: 0.8770 (tpp) cc_final: 0.8357 (tpt) REVERT: C 122 ASP cc_start: 0.9138 (m-30) cc_final: 0.8728 (m-30) REVERT: C 220 ASP cc_start: 0.8800 (t0) cc_final: 0.8336 (t70) REVERT: C 222 MET cc_start: 0.8406 (ptp) cc_final: 0.7918 (ptm) REVERT: C 282 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8263 (mtpp) REVERT: D 5 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8424 (mmpt) REVERT: D 17 GLN cc_start: 0.9077 (tp40) cc_final: 0.8729 (tp40) REVERT: D 29 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: D 68 MET cc_start: 0.8768 (tpp) cc_final: 0.8352 (tpt) REVERT: D 79 ILE cc_start: 0.9141 (pt) cc_final: 0.8866 (mm) REVERT: D 220 ASP cc_start: 0.8791 (t0) cc_final: 0.8458 (t70) REVERT: D 282 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8220 (mtpp) REVERT: E 97 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8023 (mm110) REVERT: E 122 ASP cc_start: 0.8950 (m-30) cc_final: 0.8668 (m-30) REVERT: E 191 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7131 (mt) REVERT: E 220 ASP cc_start: 0.8795 (t0) cc_final: 0.8294 (t0) REVERT: E 282 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8187 (mtpp) REVERT: F 96 ARG cc_start: 0.8871 (mtm180) cc_final: 0.8590 (mtm180) REVERT: F 97 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: F 278 GLU cc_start: 0.7693 (mp0) cc_final: 0.7201 (pm20) outliers start: 52 outliers final: 32 residues processed: 340 average time/residue: 1.3934 time to fit residues: 517.2496 Evaluate side-chains 334 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 128 ASP 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 314 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 B residue 314 SER 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 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 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 Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 111 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 159 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.144564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104178 restraints weight = 13881.823| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.49 r_work: 0.2999 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14538 Z= 0.114 Angle : 0.458 4.366 19698 Z= 0.254 Chirality : 0.046 0.163 2334 Planarity : 0.003 0.023 2496 Dihedral : 5.912 51.981 2130 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.61 % Allowed : 15.46 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1830 helix: 1.97 (0.20), residues: 714 sheet: -0.26 (0.26), residues: 408 loop : -0.30 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 162 HIS 0.003 0.001 HIS C 193 PHE 0.010 0.001 PHE C 138 TYR 0.025 0.002 TYR C 311 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 648) hydrogen bonds : angle 4.42621 ( 1800) covalent geometry : bond 0.00259 (14538) covalent geometry : angle 0.45772 (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 342 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 1.529 Fit side-chains REVERT: A 17 GLN cc_start: 0.9082 (tp40) cc_final: 0.8782 (tp40) REVERT: A 97 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: A 178 VAL cc_start: 0.8220 (m) cc_final: 0.7873 (t) REVERT: A 180 SER cc_start: 0.8179 (t) cc_final: 0.7961 (t) REVERT: A 222 MET cc_start: 0.8302 (ptp) cc_final: 0.7698 (ptp) REVERT: A 278 GLU cc_start: 0.7700 (mp0) cc_final: 0.7270 (pm20) REVERT: A 311 TYR cc_start: 0.8622 (t80) cc_final: 0.8409 (t80) REVERT: B 97 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7999 (mm110) REVERT: B 122 ASP cc_start: 0.8940 (m-30) cc_final: 0.8620 (m-30) REVERT: B 127 MET cc_start: 0.9107 (ttm) cc_final: 0.8785 (tpp) REVERT: B 191 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7124 (mt) REVERT: B 220 ASP cc_start: 0.8808 (t0) cc_final: 0.8322 (t0) REVERT: B 282 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8233 (mtpp) REVERT: C 17 GLN cc_start: 0.9068 (tp40) cc_final: 0.8772 (tp40) REVERT: C 29 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8686 (mtpt) REVERT: C 68 MET cc_start: 0.8778 (tpp) cc_final: 0.8354 (tpt) REVERT: C 122 ASP cc_start: 0.9137 (m-30) cc_final: 0.8747 (m-30) REVERT: C 222 MET cc_start: 0.8389 (ptp) cc_final: 0.8181 (ptm) REVERT: C 282 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8200 (mtpp) REVERT: D 5 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8369 (mmpt) REVERT: D 17 GLN cc_start: 0.9080 (tp40) cc_final: 0.8745 (tp40) REVERT: D 29 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8688 (mtpt) REVERT: D 68 MET cc_start: 0.8763 (tpp) cc_final: 0.8329 (tpt) REVERT: D 220 ASP cc_start: 0.8791 (t0) cc_final: 0.8457 (t70) REVERT: D 222 MET cc_start: 0.8345 (ptp) cc_final: 0.8032 (ptm) REVERT: D 282 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8183 (mtpp) REVERT: E 22 ARG cc_start: 0.8829 (mtp85) cc_final: 0.8551 (mtp85) REVERT: E 97 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8014 (mm110) REVERT: E 122 ASP cc_start: 0.8952 (m-30) cc_final: 0.8655 (m-30) REVERT: E 191 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7109 (mt) REVERT: E 220 ASP cc_start: 0.8774 (t0) cc_final: 0.8281 (t0) REVERT: F 97 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: F 278 GLU cc_start: 0.7552 (mp0) cc_final: 0.7095 (pm20) outliers start: 41 outliers final: 22 residues processed: 331 average time/residue: 1.6400 time to fit residues: 590.9702 Evaluate side-chains 325 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 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 249 THR Chi-restraints excluded: chain B residue 314 SER 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 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 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 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: 0.6980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 B 288 GLN E 283 HIS E 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103204 restraints weight = 13780.825| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.48 r_work: 0.2980 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2073 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= 0.131 Angle : 0.478 4.375 19698 Z= 0.264 Chirality : 0.047 0.162 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.887 52.896 2129 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.93 % Allowed : 15.59 % 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: 0.83 (0.20), residues: 1830 helix: 1.94 (0.20), residues: 714 sheet: -0.28 (0.26), residues: 408 loop : -0.29 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 162 HIS 0.003 0.001 HIS C 193 PHE 0.011 0.001 PHE C 138 TYR 0.023 0.002 TYR C 311 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 648) hydrogen bonds : angle 4.42878 ( 1800) covalent geometry : bond 0.00300 (14538) covalent geometry : angle 0.47756 (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 336 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 3.088 Fit side-chains REVERT: A 17 GLN cc_start: 0.9107 (tp40) cc_final: 0.8801 (tp40) REVERT: A 96 ARG cc_start: 0.8772 (mtm180) cc_final: 0.8427 (mtm180) REVERT: A 97 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7342 (mp10) REVERT: A 178 VAL cc_start: 0.8221 (m) cc_final: 0.7874 (t) REVERT: A 180 SER cc_start: 0.8186 (t) cc_final: 0.7968 (t) REVERT: A 222 MET cc_start: 0.8507 (ptp) cc_final: 0.7975 (ptp) REVERT: A 278 GLU cc_start: 0.7701 (mp0) cc_final: 0.7273 (pm20) REVERT: A 311 TYR cc_start: 0.8675 (t80) cc_final: 0.8409 (t80) REVERT: B 22 ARG cc_start: 0.8855 (mtp85) cc_final: 0.8596 (mtp85) REVERT: B 97 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8083 (mm110) REVERT: B 122 ASP cc_start: 0.8941 (m-30) cc_final: 0.8631 (m-30) REVERT: B 191 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7149 (mt) REVERT: B 205 MET cc_start: 0.5244 (ptp) cc_final: 0.4643 (ptm) REVERT: B 220 ASP cc_start: 0.8816 (t0) cc_final: 0.8303 (t0) REVERT: B 282 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8308 (mtpp) REVERT: C 17 GLN cc_start: 0.9068 (tp40) cc_final: 0.8772 (tp40) REVERT: C 29 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8717 (mtpt) REVERT: C 68 MET cc_start: 0.8777 (tpp) cc_final: 0.8365 (tpt) REVERT: C 122 ASP cc_start: 0.9139 (m-30) cc_final: 0.8738 (m-30) REVERT: C 222 MET cc_start: 0.8420 (ptp) cc_final: 0.8170 (ptm) REVERT: C 282 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8230 (mtpp) REVERT: C 314 SER cc_start: 0.6693 (OUTLIER) cc_final: 0.6236 (p) REVERT: D 5 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8365 (mmpt) REVERT: D 17 GLN cc_start: 0.9093 (tp40) cc_final: 0.8836 (tp40) REVERT: D 29 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8692 (mtpt) REVERT: D 68 MET cc_start: 0.8757 (tpp) cc_final: 0.8323 (tpt) REVERT: D 220 ASP cc_start: 0.8807 (t0) cc_final: 0.8479 (t70) REVERT: D 278 GLU cc_start: 0.7505 (mp0) cc_final: 0.7272 (mp0) REVERT: D 282 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8190 (mtpp) REVERT: E 22 ARG cc_start: 0.8867 (mtp85) cc_final: 0.8639 (mtp85) REVERT: E 97 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8018 (mm110) REVERT: E 122 ASP cc_start: 0.8950 (m-30) cc_final: 0.8654 (m-30) REVERT: E 127 MET cc_start: 0.9066 (ttm) cc_final: 0.8809 (tpp) REVERT: E 191 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7134 (mt) REVERT: E 205 MET cc_start: 0.5313 (ptp) cc_final: 0.4820 (ptm) REVERT: E 220 ASP cc_start: 0.8806 (t0) cc_final: 0.8315 (t0) REVERT: F 97 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: F 191 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7058 (mt) REVERT: F 278 GLU cc_start: 0.7644 (mp0) cc_final: 0.7187 (pm20) outliers start: 46 outliers final: 23 residues processed: 325 average time/residue: 1.4957 time to fit residues: 531.1259 Evaluate side-chains 325 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 128 ASP 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 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 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 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 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 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 191 LEU 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: 9.9990 chunk 21 optimal weight: 0.1980 chunk 80 optimal weight: 8.9990 chunk 138 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 C 38 GLN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.101539 restraints weight = 13970.120| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.47 r_work: 0.2960 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 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 = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14538 Z= 0.168 Angle : 0.517 4.408 19698 Z= 0.285 Chirality : 0.048 0.164 2334 Planarity : 0.003 0.022 2496 Dihedral : 6.065 58.115 2129 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.54 % Allowed : 16.28 % Favored : 81.17 % 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 (0.20), residues: 1830 helix: 1.87 (0.20), residues: 714 sheet: -0.30 (0.26), residues: 408 loop : -0.26 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.004 0.001 HIS C 193 PHE 0.012 0.002 PHE C 138 TYR 0.023 0.002 TYR C 311 ARG 0.003 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 648) hydrogen bonds : angle 4.51551 ( 1800) covalent geometry : bond 0.00387 (14538) covalent geometry : angle 0.51671 (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 333 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 1.719 Fit side-chains REVERT: A 17 GLN cc_start: 0.9126 (tp40) cc_final: 0.8810 (tp40) REVERT: A 97 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: A 178 VAL cc_start: 0.8245 (m) cc_final: 0.7888 (t) REVERT: A 180 SER cc_start: 0.8144 (t) cc_final: 0.7929 (t) REVERT: A 222 MET cc_start: 0.8456 (ptp) cc_final: 0.7864 (ptp) REVERT: A 278 GLU cc_start: 0.7723 (mp0) cc_final: 0.7309 (pm20) REVERT: A 311 TYR cc_start: 0.8702 (t80) cc_final: 0.8440 (t80) REVERT: B 22 ARG cc_start: 0.8914 (mtp85) cc_final: 0.8693 (mtp85) REVERT: B 97 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8021 (mm110) REVERT: B 122 ASP cc_start: 0.8944 (m-30) cc_final: 0.8650 (m-30) REVERT: B 127 MET cc_start: 0.9057 (ttm) cc_final: 0.8769 (tpp) REVERT: B 191 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7197 (mt) REVERT: B 220 ASP cc_start: 0.8838 (t0) cc_final: 0.8318 (t0) REVERT: B 282 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8262 (mtpp) REVERT: C 29 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8687 (mtpt) REVERT: C 68 MET cc_start: 0.8798 (tpp) cc_final: 0.8366 (tpt) REVERT: C 122 ASP cc_start: 0.9136 (m-30) cc_final: 0.8769 (m-30) REVERT: C 222 MET cc_start: 0.8412 (ptp) cc_final: 0.8151 (ptm) REVERT: C 282 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8251 (mtpp) REVERT: C 314 SER cc_start: 0.6706 (OUTLIER) cc_final: 0.6245 (p) REVERT: D 5 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8384 (mmpt) REVERT: D 17 GLN cc_start: 0.9072 (tp40) cc_final: 0.8821 (tp40) REVERT: D 29 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8640 (mtpt) REVERT: D 68 MET cc_start: 0.8790 (tpp) cc_final: 0.8423 (tpt) REVERT: D 220 ASP cc_start: 0.8821 (t0) cc_final: 0.8473 (t70) REVERT: D 278 GLU cc_start: 0.7533 (mp0) cc_final: 0.7293 (mp0) REVERT: D 282 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: E 22 ARG cc_start: 0.8898 (mtp85) cc_final: 0.8664 (mtp85) REVERT: E 97 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8030 (mm110) REVERT: E 122 ASP cc_start: 0.8964 (m-30) cc_final: 0.8709 (m-30) REVERT: E 127 MET cc_start: 0.9119 (ttm) cc_final: 0.8873 (tpp) REVERT: E 191 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7180 (mt) REVERT: E 220 ASP cc_start: 0.8834 (t0) cc_final: 0.8321 (t0) REVERT: F 97 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: F 191 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7088 (mt) REVERT: F 278 GLU cc_start: 0.7685 (mp0) cc_final: 0.7241 (pm20) outliers start: 40 outliers final: 25 residues processed: 324 average time/residue: 1.3801 time to fit residues: 488.2530 Evaluate side-chains 330 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 128 ASP 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 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 38 GLN 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 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 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 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 191 LEU 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 121 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 120 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.144731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104479 restraints weight = 13916.356| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.48 r_work: 0.3005 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 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 = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14538 Z= 0.110 Angle : 0.461 4.380 19698 Z= 0.255 Chirality : 0.046 0.163 2334 Planarity : 0.003 0.022 2496 Dihedral : 5.867 59.747 2129 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.23 % Allowed : 16.48 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1830 helix: 1.92 (0.20), residues: 714 sheet: -0.31 (0.26), residues: 408 loop : -0.29 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 162 HIS 0.002 0.001 HIS C 193 PHE 0.010 0.001 PHE E 138 TYR 0.027 0.002 TYR C 311 ARG 0.003 0.000 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 648) hydrogen bonds : angle 4.41725 ( 1800) covalent geometry : bond 0.00247 (14538) covalent geometry : angle 0.46066 (19698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15323.02 seconds wall clock time: 268 minutes 20.03 seconds (16100.03 seconds total)