Starting phenix.real_space_refine on Tue Dec 31 00:27:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbl_27289/12_2024/8dbl_27289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbl_27289/12_2024/8dbl_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_27289/12_2024/8dbl_27289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbl_27289/12_2024/8dbl_27289.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbl_27289/12_2024/8dbl_27289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbl_27289/12_2024/8dbl_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.69, 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: 3.67 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: 1.74 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: 4.55 Time building geometry restraints manager: 4.15 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.140 Process input model: 33.760 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.360 ------------------------------------------------------------------------------- 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= 0.737 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 *********************** 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 : 1.581 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: 1.4501 time to fit residues: 556.9154 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 : 1.536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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= 0.203 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 : 7.54 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 *********************** 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 : 1.466 Fit side-chains REVERT: A 5 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8435 (mmpt) REVERT: A 17 GLN cc_start: 0.9013 (tp40) cc_final: 0.8752 (tp40) REVERT: A 68 MET cc_start: 0.8457 (tpp) cc_final: 0.8224 (mmm) REVERT: A 96 ARG cc_start: 0.6736 (mtm180) cc_final: 0.6452 (mtm180) REVERT: A 97 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: A 115 MET cc_start: 0.8636 (mtp) cc_final: 0.8402 (mtp) REVERT: A 127 MET cc_start: 0.8498 (ttm) cc_final: 0.8203 (ttm) REVERT: A 178 VAL cc_start: 0.8047 (m) cc_final: 0.7623 (t) REVERT: A 180 SER cc_start: 0.8508 (t) cc_final: 0.8305 (t) REVERT: A 220 ASP cc_start: 0.8448 (t0) cc_final: 0.8221 (t70) REVERT: A 222 MET cc_start: 0.8012 (ptp) cc_final: 0.7442 (ptp) REVERT: B 97 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6940 (mm110) REVERT: B 122 ASP cc_start: 0.8371 (m-30) cc_final: 0.8133 (m-30) REVERT: B 220 ASP cc_start: 0.8518 (t0) cc_final: 0.8044 (t0) REVERT: C 17 GLN cc_start: 0.8972 (tp40) cc_final: 0.8665 (tp40) REVERT: C 68 MET cc_start: 0.8278 (tpp) cc_final: 0.8026 (tpt) REVERT: C 122 ASP cc_start: 0.8640 (m-30) cc_final: 0.8390 (m-30) REVERT: C 220 ASP cc_start: 0.8537 (t0) cc_final: 0.8202 (t70) REVERT: D 17 GLN cc_start: 0.8991 (tp40) cc_final: 0.8691 (tp40) REVERT: D 68 MET cc_start: 0.8278 (tpp) cc_final: 0.8020 (tpt) REVERT: D 79 ILE cc_start: 0.9079 (pt) cc_final: 0.8865 (mm) REVERT: D 158 ASN cc_start: 0.7453 (m-40) cc_final: 0.7231 (m-40) REVERT: D 220 ASP cc_start: 0.8539 (t0) cc_final: 0.8214 (t70) REVERT: E 97 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6926 (mm110) REVERT: E 122 ASP cc_start: 0.8369 (m-30) cc_final: 0.8153 (m-30) REVERT: E 220 ASP cc_start: 0.8521 (t0) cc_final: 0.8042 (t0) REVERT: F 5 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8476 (mmpt) REVERT: F 68 MET cc_start: 0.8487 (tpp) cc_final: 0.8257 (mmm) REVERT: F 97 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6496 (mp10) REVERT: F 115 MET cc_start: 0.8626 (mtp) cc_final: 0.8390 (mtp) REVERT: F 127 MET cc_start: 0.8490 (ttm) cc_final: 0.8191 (ttm) REVERT: F 220 ASP cc_start: 0.8445 (t0) cc_final: 0.8216 (t70) REVERT: F 222 MET cc_start: 0.7864 (ptp) cc_final: 0.7511 (ptp) outliers start: 75 outliers final: 24 residues processed: 368 average time/residue: 1.3702 time to fit residues: 549.8263 Evaluate side-chains 325 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 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 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 90 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN 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 17 GLN E 97 GLN E 283 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14538 Z= 0.222 Angle : 0.504 4.184 19698 Z= 0.276 Chirality : 0.047 0.166 2334 Planarity : 0.003 0.021 2496 Dihedral : 7.039 50.645 2144 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.12 % Allowed : 15.08 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1830 helix: 1.88 (0.20), residues: 714 sheet: -0.29 (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 193 PHE 0.011 0.002 PHE D 138 TYR 0.016 0.002 TYR A 311 ARG 0.002 0.000 ARG B 260 *********************** 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 351 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 1.596 Fit side-chains REVERT: A 17 GLN cc_start: 0.9037 (tp40) cc_final: 0.8784 (tp40) REVERT: A 68 MET cc_start: 0.8490 (tpp) cc_final: 0.8258 (mmm) REVERT: A 97 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6502 (mp10) REVERT: A 115 MET cc_start: 0.8665 (mtp) cc_final: 0.8415 (mtp) REVERT: A 127 MET cc_start: 0.8516 (ttm) cc_final: 0.8303 (ttm) REVERT: A 178 VAL cc_start: 0.8069 (m) cc_final: 0.7653 (t) REVERT: A 220 ASP cc_start: 0.8521 (t0) cc_final: 0.8248 (t70) REVERT: A 222 MET cc_start: 0.8019 (ptp) cc_final: 0.7467 (ptp) REVERT: A 259 SER cc_start: 0.8568 (p) cc_final: 0.8301 (p) REVERT: B 122 ASP cc_start: 0.8378 (m-30) cc_final: 0.8144 (m-30) REVERT: B 220 ASP cc_start: 0.8559 (t0) cc_final: 0.8140 (t0) REVERT: C 68 MET cc_start: 0.8392 (tpp) cc_final: 0.8073 (tpt) REVERT: C 122 ASP cc_start: 0.8604 (m-30) cc_final: 0.8355 (m-30) REVERT: C 220 ASP cc_start: 0.8594 (t0) cc_final: 0.8252 (t70) REVERT: C 222 MET cc_start: 0.8125 (ptp) cc_final: 0.7736 (ptm) REVERT: C 281 MET cc_start: 0.7147 (mtp) cc_final: 0.6870 (mtp) REVERT: D 17 GLN cc_start: 0.9004 (tp40) cc_final: 0.8742 (tp40) REVERT: D 68 MET cc_start: 0.8390 (tpp) cc_final: 0.8062 (tpt) REVERT: D 158 ASN cc_start: 0.7414 (m-40) cc_final: 0.7202 (m-40) REVERT: D 220 ASP cc_start: 0.8598 (t0) cc_final: 0.8309 (t70) REVERT: D 222 MET cc_start: 0.8087 (ptp) cc_final: 0.7821 (ptm) REVERT: E 122 ASP cc_start: 0.8372 (m-30) cc_final: 0.8158 (m-30) REVERT: E 220 ASP cc_start: 0.8539 (t0) cc_final: 0.8113 (t0) REVERT: F 68 MET cc_start: 0.8492 (tpp) cc_final: 0.8260 (mmm) REVERT: F 97 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6573 (mp10) REVERT: F 115 MET cc_start: 0.8655 (mtp) cc_final: 0.8400 (mtp) REVERT: F 127 MET cc_start: 0.8527 (ttm) cc_final: 0.8314 (ttm) REVERT: F 220 ASP cc_start: 0.8541 (t0) cc_final: 0.8252 (t70) REVERT: F 259 SER cc_start: 0.8546 (p) cc_final: 0.8306 (p) outliers start: 49 outliers final: 23 residues processed: 330 average time/residue: 1.4248 time to fit residues: 512.1687 Evaluate side-chains 315 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 290 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 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 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 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 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 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 161 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 0.0870 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 283 HIS ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14538 Z= 0.210 Angle : 0.491 4.283 19698 Z= 0.270 Chirality : 0.047 0.165 2334 Planarity : 0.003 0.022 2496 Dihedral : 6.502 44.042 2130 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 15.59 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1830 helix: 1.90 (0.20), residues: 714 sheet: -0.09 (0.26), residues: 408 loop : -0.25 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 162 HIS 0.003 0.001 HIS E 193 PHE 0.011 0.001 PHE C 138 TYR 0.018 0.002 TYR B 311 ARG 0.002 0.000 ARG B 49 *********************** 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 343 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 1.718 Fit side-chains REVERT: A 17 GLN cc_start: 0.9014 (tp40) cc_final: 0.8778 (tp40) REVERT: A 68 MET cc_start: 0.8491 (tpp) cc_final: 0.8255 (mmm) REVERT: A 97 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6578 (mp10) REVERT: A 127 MET cc_start: 0.8516 (ttm) cc_final: 0.8253 (ttm) REVERT: A 178 VAL cc_start: 0.8014 (m) cc_final: 0.7583 (t) REVERT: A 220 ASP cc_start: 0.8517 (t0) cc_final: 0.8228 (t70) REVERT: A 222 MET cc_start: 0.8112 (ptp) cc_final: 0.7522 (ptp) REVERT: A 259 SER cc_start: 0.8540 (p) cc_final: 0.8315 (p) REVERT: B 35 PHE cc_start: 0.7592 (m-80) cc_final: 0.7368 (m-80) REVERT: B 97 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6816 (mm110) REVERT: B 122 ASP cc_start: 0.8371 (m-30) cc_final: 0.8139 (m-30) REVERT: B 127 MET cc_start: 0.8523 (ttm) cc_final: 0.8300 (tpp) REVERT: B 220 ASP cc_start: 0.8573 (t0) cc_final: 0.8153 (t0) REVERT: C 38 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6618 (mp-120) REVERT: C 68 MET cc_start: 0.8395 (tpp) cc_final: 0.8083 (tpt) REVERT: C 122 ASP cc_start: 0.8601 (m-30) cc_final: 0.8371 (m-30) REVERT: C 220 ASP cc_start: 0.8642 (t0) cc_final: 0.8268 (t70) REVERT: C 222 MET cc_start: 0.8142 (ptp) cc_final: 0.7751 (ptm) REVERT: D 17 GLN cc_start: 0.9010 (tp40) cc_final: 0.8784 (tp40) REVERT: D 68 MET cc_start: 0.8395 (tpp) cc_final: 0.8075 (tpt) REVERT: D 220 ASP cc_start: 0.8644 (t0) cc_final: 0.8334 (t70) REVERT: D 222 MET cc_start: 0.8118 (ptp) cc_final: 0.7823 (ptm) REVERT: E 97 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6974 (mm110) REVERT: E 122 ASP cc_start: 0.8362 (m-30) cc_final: 0.8154 (m-30) REVERT: E 127 MET cc_start: 0.8521 (ttm) cc_final: 0.8298 (tpp) REVERT: E 191 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7051 (mt) REVERT: E 220 ASP cc_start: 0.8562 (t0) cc_final: 0.8121 (t0) REVERT: F 68 MET cc_start: 0.8488 (tpp) cc_final: 0.8251 (mmm) REVERT: F 115 MET cc_start: 0.8647 (mtp) cc_final: 0.8396 (mtp) REVERT: F 127 MET cc_start: 0.8506 (ttm) cc_final: 0.8247 (ttm) REVERT: F 259 SER cc_start: 0.8516 (p) cc_final: 0.8297 (p) outliers start: 47 outliers final: 26 residues processed: 322 average time/residue: 1.4396 time to fit residues: 505.7676 Evaluate side-chains 320 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain A residue 249 THR 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 38 GLN 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 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 E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 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 144 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 283 HIS E 283 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14538 Z= 0.200 Angle : 0.481 4.277 19698 Z= 0.264 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.023 2496 Dihedral : 6.269 48.935 2130 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.50 % Allowed : 15.01 % 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: 0.89 (0.20), residues: 1830 helix: 1.94 (0.20), residues: 714 sheet: -0.13 (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 E 162 HIS 0.003 0.001 HIS B 193 PHE 0.012 0.001 PHE B 35 TYR 0.018 0.002 TYR E 311 ARG 0.002 0.000 ARG A 96 *********************** 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 364 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 309 time to evaluate : 1.640 Fit side-chains REVERT: A 17 GLN cc_start: 0.9022 (tp40) cc_final: 0.8781 (tp40) REVERT: A 68 MET cc_start: 0.8486 (tpp) cc_final: 0.8251 (mmm) REVERT: A 127 MET cc_start: 0.8509 (ttm) cc_final: 0.8287 (ttm) REVERT: A 178 VAL cc_start: 0.8001 (m) cc_final: 0.7589 (t) REVERT: A 222 MET cc_start: 0.8030 (ptp) cc_final: 0.7617 (ptp) REVERT: A 259 SER cc_start: 0.8523 (p) cc_final: 0.8296 (p) REVERT: B 97 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6963 (mm110) REVERT: B 122 ASP cc_start: 0.8358 (m-30) cc_final: 0.8136 (m-30) REVERT: B 191 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7057 (mt) REVERT: B 220 ASP cc_start: 0.8602 (t0) cc_final: 0.8185 (t0) REVERT: C 68 MET cc_start: 0.8393 (tpp) cc_final: 0.8042 (tpt) REVERT: C 220 ASP cc_start: 0.8637 (t0) cc_final: 0.8217 (t70) REVERT: C 222 MET cc_start: 0.8187 (ptp) cc_final: 0.7767 (ptm) REVERT: C 314 SER cc_start: 0.6010 (OUTLIER) cc_final: 0.5607 (p) REVERT: D 17 GLN cc_start: 0.9005 (tp40) cc_final: 0.8780 (tp40) REVERT: D 68 MET cc_start: 0.8391 (tpp) cc_final: 0.8039 (tpt) REVERT: D 220 ASP cc_start: 0.8641 (t0) cc_final: 0.8298 (t70) REVERT: D 222 MET cc_start: 0.8161 (ptp) cc_final: 0.7859 (ptm) REVERT: D 314 SER cc_start: 0.5963 (OUTLIER) cc_final: 0.5575 (p) REVERT: E 97 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6968 (mm110) REVERT: E 122 ASP cc_start: 0.8359 (m-30) cc_final: 0.8154 (m-30) REVERT: E 191 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7181 (mt) REVERT: E 220 ASP cc_start: 0.8576 (t0) cc_final: 0.8143 (t0) REVERT: F 68 MET cc_start: 0.8494 (tpp) cc_final: 0.8247 (mmm) REVERT: F 97 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: F 127 MET cc_start: 0.8522 (ttm) cc_final: 0.8299 (ttm) REVERT: F 259 SER cc_start: 0.8504 (p) cc_final: 0.8289 (p) outliers start: 55 outliers final: 23 residues processed: 346 average time/residue: 1.3106 time to fit residues: 495.8356 Evaluate side-chains 317 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 287 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 174 optimal weight: 0.1980 chunk 144 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 283 HIS E 283 HIS E 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14538 Z= 0.148 Angle : 0.445 4.263 19698 Z= 0.245 Chirality : 0.046 0.164 2334 Planarity : 0.002 0.024 2496 Dihedral : 5.969 59.734 2130 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.12 % Allowed : 15.39 % 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: 0.94 (0.20), residues: 1830 helix: 2.05 (0.20), residues: 714 sheet: -0.15 (0.26), residues: 408 loop : -0.32 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 162 HIS 0.003 0.001 HIS B 193 PHE 0.010 0.001 PHE C 138 TYR 0.022 0.002 TYR C 311 ARG 0.002 0.000 ARG D 49 *********************** 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 348 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 1.785 Fit side-chains REVERT: A 17 GLN cc_start: 0.8986 (tp40) cc_final: 0.8764 (tp40) REVERT: A 68 MET cc_start: 0.8476 (tpp) cc_final: 0.8268 (mmm) REVERT: A 97 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6163 (mp10) REVERT: A 178 VAL cc_start: 0.8100 (m) cc_final: 0.7696 (t) REVERT: A 222 MET cc_start: 0.8103 (ptp) cc_final: 0.7630 (ptp) REVERT: B 97 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6750 (mm110) REVERT: B 122 ASP cc_start: 0.8339 (m-30) cc_final: 0.8083 (m-30) REVERT: B 127 MET cc_start: 0.8433 (ttm) cc_final: 0.8219 (tpp) REVERT: B 220 ASP cc_start: 0.8582 (t0) cc_final: 0.8161 (t0) REVERT: C 68 MET cc_start: 0.8374 (tpp) cc_final: 0.8031 (tpt) REVERT: C 122 ASP cc_start: 0.8603 (m-30) cc_final: 0.8345 (m-30) REVERT: C 222 MET cc_start: 0.8035 (ptp) cc_final: 0.7816 (ptm) REVERT: D 5 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8179 (mmpt) REVERT: D 17 GLN cc_start: 0.8975 (tp40) cc_final: 0.8738 (tp40) REVERT: D 68 MET cc_start: 0.8369 (tpp) cc_final: 0.8016 (tpt) REVERT: D 220 ASP cc_start: 0.8632 (t0) cc_final: 0.8282 (t70) REVERT: D 222 MET cc_start: 0.8014 (ptp) cc_final: 0.7734 (ptm) REVERT: E 97 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6815 (mm110) REVERT: E 122 ASP cc_start: 0.8336 (m-30) cc_final: 0.8114 (m-30) REVERT: E 127 MET cc_start: 0.8430 (ttm) cc_final: 0.8220 (tpp) REVERT: E 191 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7186 (mt) REVERT: E 220 ASP cc_start: 0.8550 (t0) cc_final: 0.8138 (t0) REVERT: F 68 MET cc_start: 0.8484 (tpp) cc_final: 0.8253 (mmm) REVERT: F 259 SER cc_start: 0.8479 (p) cc_final: 0.8269 (p) outliers start: 49 outliers final: 23 residues processed: 336 average time/residue: 1.3495 time to fit residues: 495.1460 Evaluate side-chains 328 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 5 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 127 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 B 288 GLN D 283 HIS E 283 HIS E 288 GLN F 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2087 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= 0.181 Angle : 0.468 4.331 19698 Z= 0.257 Chirality : 0.047 0.163 2334 Planarity : 0.003 0.027 2496 Dihedral : 5.933 59.804 2130 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.61 % Allowed : 16.09 % 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: 0.97 (0.20), residues: 1830 helix: 2.07 (0.20), residues: 714 sheet: -0.16 (0.26), residues: 408 loop : -0.27 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 162 HIS 0.004 0.001 HIS B 193 PHE 0.010 0.001 PHE D 138 TYR 0.020 0.002 TYR F 311 ARG 0.007 0.000 ARG A 184 *********************** 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 332 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 1.471 Fit side-chains REVERT: A 17 GLN cc_start: 0.8996 (tp40) cc_final: 0.8707 (tp40) REVERT: A 97 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.6168 (mp10) REVERT: A 178 VAL cc_start: 0.8105 (m) cc_final: 0.7699 (t) REVERT: A 222 MET cc_start: 0.8115 (ptp) cc_final: 0.7619 (ptp) REVERT: B 97 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6833 (mm110) REVERT: B 122 ASP cc_start: 0.8341 (m-30) cc_final: 0.8100 (m-30) REVERT: B 127 MET cc_start: 0.8503 (ttm) cc_final: 0.8121 (tpp) REVERT: B 220 ASP cc_start: 0.8606 (t0) cc_final: 0.8167 (t0) REVERT: C 68 MET cc_start: 0.8406 (tpp) cc_final: 0.8036 (tpt) REVERT: C 122 ASP cc_start: 0.8617 (m-30) cc_final: 0.8313 (m-30) REVERT: C 220 ASP cc_start: 0.8624 (t0) cc_final: 0.8203 (t70) REVERT: C 222 MET cc_start: 0.8130 (ptp) cc_final: 0.7696 (ptm) REVERT: D 5 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8173 (mmpt) REVERT: D 68 MET cc_start: 0.8395 (tpp) cc_final: 0.8026 (tpt) REVERT: D 220 ASP cc_start: 0.8657 (t0) cc_final: 0.8342 (t70) REVERT: D 222 MET cc_start: 0.8089 (ptp) cc_final: 0.7799 (ptm) REVERT: D 314 SER cc_start: 0.5755 (OUTLIER) cc_final: 0.5384 (p) REVERT: E 97 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6832 (mm110) REVERT: E 122 ASP cc_start: 0.8342 (m-30) cc_final: 0.8127 (m-30) REVERT: E 127 MET cc_start: 0.8498 (ttm) cc_final: 0.8298 (tpp) REVERT: E 191 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7226 (mt) REVERT: E 220 ASP cc_start: 0.8596 (t0) cc_final: 0.8184 (t0) REVERT: F 68 MET cc_start: 0.8497 (tpp) cc_final: 0.8256 (mmm) REVERT: F 259 SER cc_start: 0.8469 (p) cc_final: 0.8259 (p) outliers start: 41 outliers final: 25 residues processed: 324 average time/residue: 1.4171 time to fit residues: 501.4271 Evaluate side-chains 314 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 43 GLU 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 C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 118 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 283 HIS B 283 HIS B 288 GLN C 17 GLN C 283 HIS D 283 HIS E 283 HIS E 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2141 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= 0.181 Angle : 0.465 4.349 19698 Z= 0.256 Chirality : 0.047 0.163 2334 Planarity : 0.003 0.028 2496 Dihedral : 5.800 49.435 2130 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.05 % Allowed : 15.52 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1830 helix: 2.07 (0.20), residues: 714 sheet: -0.17 (0.26), residues: 408 loop : -0.25 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 162 HIS 0.003 0.001 HIS B 193 PHE 0.010 0.001 PHE C 138 TYR 0.021 0.002 TYR E 311 ARG 0.006 0.000 ARG A 184 *********************** 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 331 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 1.563 Fit side-chains REVERT: A 17 GLN cc_start: 0.8997 (tp40) cc_final: 0.8767 (tp40) REVERT: A 97 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: A 178 VAL cc_start: 0.8108 (m) cc_final: 0.7698 (t) REVERT: A 222 MET cc_start: 0.8105 (ptp) cc_final: 0.7609 (ptp) REVERT: B 97 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6827 (mm110) REVERT: B 122 ASP cc_start: 0.8344 (m-30) cc_final: 0.8100 (m-30) REVERT: B 127 MET cc_start: 0.8504 (ttm) cc_final: 0.8112 (tpp) REVERT: B 220 ASP cc_start: 0.8611 (t0) cc_final: 0.8191 (t0) REVERT: C 68 MET cc_start: 0.8400 (tpp) cc_final: 0.8071 (tpt) REVERT: C 122 ASP cc_start: 0.8621 (m-30) cc_final: 0.8376 (m-30) REVERT: C 222 MET cc_start: 0.8122 (ptp) cc_final: 0.7900 (ptm) REVERT: C 314 SER cc_start: 0.5852 (OUTLIER) cc_final: 0.5464 (p) REVERT: D 5 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8147 (mmpt) REVERT: D 68 MET cc_start: 0.8399 (tpp) cc_final: 0.8024 (tpt) REVERT: D 220 ASP cc_start: 0.8661 (t0) cc_final: 0.8345 (t70) REVERT: D 222 MET cc_start: 0.8060 (ptp) cc_final: 0.7771 (ptm) REVERT: D 314 SER cc_start: 0.5801 (OUTLIER) cc_final: 0.5453 (p) REVERT: E 22 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8424 (mtp85) REVERT: E 97 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6829 (mm110) REVERT: E 122 ASP cc_start: 0.8343 (m-30) cc_final: 0.8125 (m-30) REVERT: E 127 MET cc_start: 0.8496 (ttm) cc_final: 0.8108 (tpp) REVERT: E 191 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7224 (mt) REVERT: E 205 MET cc_start: 0.3757 (ptp) cc_final: 0.3345 (ptm) REVERT: E 220 ASP cc_start: 0.8604 (t0) cc_final: 0.8186 (t0) REVERT: F 68 MET cc_start: 0.8502 (tpp) cc_final: 0.8270 (mmm) REVERT: F 97 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6163 (mp10) REVERT: F 259 SER cc_start: 0.8471 (p) cc_final: 0.8259 (p) outliers start: 48 outliers final: 27 residues processed: 318 average time/residue: 1.4626 time to fit residues: 506.5711 Evaluate side-chains 322 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 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 259 SER Chi-restraints excluded: chain C residue 118 VAL 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 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 259 SER 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 157 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 C 38 GLN D 283 HIS E 283 HIS E 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2033 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= 0.237 Angle : 0.508 4.393 19698 Z= 0.278 Chirality : 0.048 0.165 2334 Planarity : 0.003 0.028 2496 Dihedral : 5.914 51.869 2130 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.86 % Allowed : 16.22 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1830 helix: 2.01 (0.20), residues: 714 sheet: -0.18 (0.26), residues: 408 loop : -0.25 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 162 HIS 0.004 0.001 HIS B 193 PHE 0.011 0.002 PHE D 138 TYR 0.020 0.002 TYR E 311 ARG 0.006 0.000 ARG A 184 *********************** 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 334 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 289 time to evaluate : 1.656 Fit side-chains REVERT: A 17 GLN cc_start: 0.9040 (tp40) cc_final: 0.8748 (tp40) REVERT: A 97 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.6121 (mp10) REVERT: A 178 VAL cc_start: 0.7996 (m) cc_final: 0.7588 (t) REVERT: A 222 MET cc_start: 0.8214 (ptp) cc_final: 0.7735 (ptp) REVERT: B 97 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6853 (mm110) REVERT: B 122 ASP cc_start: 0.8377 (m-30) cc_final: 0.8157 (m-30) REVERT: B 220 ASP cc_start: 0.8630 (t0) cc_final: 0.8199 (t0) REVERT: C 68 MET cc_start: 0.8410 (tpp) cc_final: 0.8054 (tpt) REVERT: C 220 ASP cc_start: 0.8651 (t0) cc_final: 0.8225 (t70) REVERT: C 222 MET cc_start: 0.8155 (ptp) cc_final: 0.7696 (ptm) REVERT: C 314 SER cc_start: 0.5850 (OUTLIER) cc_final: 0.5457 (p) REVERT: D 5 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8145 (mmpt) REVERT: D 68 MET cc_start: 0.8427 (tpp) cc_final: 0.8084 (tpt) REVERT: D 220 ASP cc_start: 0.8651 (t0) cc_final: 0.8333 (t70) REVERT: D 222 MET cc_start: 0.8120 (ptp) cc_final: 0.7782 (ptm) REVERT: D 314 SER cc_start: 0.5766 (OUTLIER) cc_final: 0.5412 (p) REVERT: E 97 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6850 (mm110) REVERT: E 122 ASP cc_start: 0.8375 (m-30) cc_final: 0.8170 (m-30) REVERT: E 191 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7248 (mt) REVERT: E 205 MET cc_start: 0.3717 (ptp) cc_final: 0.3217 (ptm) REVERT: E 220 ASP cc_start: 0.8607 (t0) cc_final: 0.8188 (t0) REVERT: F 68 MET cc_start: 0.8501 (tpp) cc_final: 0.8254 (mmm) REVERT: F 97 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.6096 (mp10) REVERT: F 259 SER cc_start: 0.8459 (p) cc_final: 0.8255 (p) outliers start: 45 outliers final: 30 residues processed: 323 average time/residue: 1.3864 time to fit residues: 488.9012 Evaluate side-chains 312 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 A residue 259 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 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 259 SER 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 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 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 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 D 283 HIS E 283 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2155 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= 0.185 Angle : 0.475 4.469 19698 Z= 0.262 Chirality : 0.047 0.164 2334 Planarity : 0.003 0.027 2496 Dihedral : 5.783 52.398 2130 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.74 % Allowed : 16.86 % Favored : 80.41 % 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: 0.91 (0.20), residues: 1830 helix: 2.01 (0.20), residues: 714 sheet: -0.20 (0.26), residues: 408 loop : -0.29 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.003 0.001 HIS B 193 PHE 0.010 0.001 PHE C 138 TYR 0.027 0.002 TYR C 311 ARG 0.006 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 1.676 Fit side-chains REVERT: A 17 GLN cc_start: 0.9004 (tp40) cc_final: 0.8769 (tp40) REVERT: A 97 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6190 (mp10) REVERT: A 178 VAL cc_start: 0.7982 (m) cc_final: 0.7583 (t) REVERT: A 222 MET cc_start: 0.8067 (ptp) cc_final: 0.7585 (ptp) REVERT: B 97 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6833 (mm110) REVERT: B 122 ASP cc_start: 0.8349 (m-30) cc_final: 0.8120 (m-30) REVERT: B 127 MET cc_start: 0.8446 (ttm) cc_final: 0.8185 (tpp) REVERT: B 220 ASP cc_start: 0.8595 (t0) cc_final: 0.8193 (t0) REVERT: C 68 MET cc_start: 0.8390 (tpp) cc_final: 0.8027 (tpt) REVERT: C 122 ASP cc_start: 0.8613 (m-30) cc_final: 0.8371 (m-30) REVERT: C 222 MET cc_start: 0.8121 (ptp) cc_final: 0.7886 (ptm) REVERT: C 314 SER cc_start: 0.5854 (OUTLIER) cc_final: 0.5456 (p) REVERT: D 5 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8104 (mmpt) REVERT: D 68 MET cc_start: 0.8385 (tpp) cc_final: 0.8013 (tpt) REVERT: D 220 ASP cc_start: 0.8640 (t0) cc_final: 0.8334 (t70) REVERT: D 222 MET cc_start: 0.8095 (ptp) cc_final: 0.7784 (ptm) REVERT: D 314 SER cc_start: 0.5800 (OUTLIER) cc_final: 0.5461 (p) REVERT: E 97 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6839 (mm110) REVERT: E 122 ASP cc_start: 0.8364 (m-30) cc_final: 0.8158 (m-30) REVERT: E 127 MET cc_start: 0.8457 (ttm) cc_final: 0.8201 (tpp) REVERT: E 191 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7212 (mt) REVERT: E 205 MET cc_start: 0.3768 (ptp) cc_final: 0.3327 (ptm) REVERT: E 220 ASP cc_start: 0.8612 (t0) cc_final: 0.8182 (t0) REVERT: F 68 MET cc_start: 0.8501 (tpp) cc_final: 0.8282 (mmm) REVERT: F 96 ARG cc_start: 0.6447 (mtm180) cc_final: 0.6093 (mtm180) REVERT: F 97 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6141 (mp10) outliers start: 43 outliers final: 26 residues processed: 313 average time/residue: 1.4283 time to fit residues: 487.0431 Evaluate side-chains 320 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain B residue 97 GLN 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 259 SER 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 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 143 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.161043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.122233 restraints weight = 13682.288| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.48 r_work: 0.3239 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 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 = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14538 Z= 0.181 Angle : 0.471 4.425 19698 Z= 0.260 Chirality : 0.047 0.163 2334 Planarity : 0.003 0.026 2496 Dihedral : 5.718 51.507 2130 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 16.67 % Favored : 80.79 % 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: 0.92 (0.20), residues: 1830 helix: 2.02 (0.20), residues: 714 sheet: -0.19 (0.26), residues: 408 loop : -0.28 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 162 HIS 0.003 0.001 HIS B 193 PHE 0.010 0.001 PHE C 138 TYR 0.026 0.002 TYR C 311 ARG 0.006 0.000 ARG A 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7266.27 seconds wall clock time: 130 minutes 33.86 seconds (7833.86 seconds total)