Starting phenix.real_space_refine on Sat Sep 12 10:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t1y_10363/09_2026/6t1y_10363.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t1y_10363/09_2026/6t1y_10363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t1y_10363/09_2026/6t1y_10363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t1y_10363/09_2026/6t1y_10363.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6t1y_10363/09_2026/6t1y_10363.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t1y_10363/09_2026/6t1y_10363.cif" model { file = "/net/cci-nas-00/data/ceres_data/6t1y_10363/09_2026/6t1y_10363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t1y_10363/09_2026/6t1y_10363.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.018 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 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9410 2.51 5 N 2510 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14915 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.98, per 1000 atoms: 0.20 Number of scatterers: 14915 At special positions: 0 Unit cell: (94.62, 90.06, 192.66, 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 110 16.00 P 10 15.00 Mg 5 11.99 O 2870 8.00 N 2510 7.00 C 9410 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 Links applied TRANS " TRP F 1 " - " ALA F 7 " " DTH F 4 " - " ALA F 3 " " TRP G 1 " - " ALA G 7 " " DTH G 4 " - " ALA G 3 " " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 678.7 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH F 4 " pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3490 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 30 sheets defined 49.1% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 124 removed outlier: 4.011A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 124 removed outlier: 4.011A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 124 removed outlier: 4.011A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 124 removed outlier: 4.012A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 351 through 356 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 124 removed outlier: 4.011A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 232 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.623A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.047A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.622A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.046A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.622A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.046A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.621A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.045A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.623A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.045A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 745 hydrogen bonds defined for protein. 1815 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: 2.70 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3772 1.32 - 1.44: 3417 1.44 - 1.56: 7856 1.56 - 1.68: 5 1.68 - 1.81: 190 Bond restraints: 15240 Sorted by residual: bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" CA EEP G 2 " pdb=" C EEP G 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" CA EEP F 2 " pdb=" C EEP F 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18109 2.18 - 4.36: 2188 4.36 - 6.54: 243 6.54 - 8.72: 109 8.72 - 10.90: 41 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C ALA A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta sigma weight residual 119.66 128.66 -9.00 7.30e-01 1.88e+00 1.52e+02 angle pdb=" C ALA E 331 " pdb=" N PRO E 332 " pdb=" CA PRO E 332 " ideal model delta sigma weight residual 119.66 128.64 -8.98 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA C 331 " pdb=" N PRO C 332 " pdb=" CA PRO C 332 " ideal model delta sigma weight residual 119.66 128.64 -8.98 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA D 331 " pdb=" N PRO D 332 " pdb=" CA PRO D 332 " ideal model delta sigma weight residual 119.66 128.63 -8.97 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta sigma weight residual 119.66 128.56 -8.90 7.30e-01 1.88e+00 1.49e+02 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.95: 8984 29.95 - 59.90: 96 59.90 - 89.86: 45 89.86 - 119.81: 0 119.81 - 149.76: 10 Dihedral angle restraints: 9135 sinusoidal: 3680 harmonic: 5455 Sorted by residual: dihedral pdb=" O1B ADP C 376 " pdb=" O3A ADP C 376 " pdb=" PB ADP C 376 " pdb=" PA ADP C 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.76 -149.76 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP D 376 " pdb=" O3A ADP D 376 " pdb=" PB ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.74 -149.74 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP A 376 " pdb=" O3A ADP A 376 " pdb=" PB ADP A 376 " pdb=" PA ADP A 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.73 -149.73 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.021: 2295 1.021 - 2.043: 0 2.043 - 3.064: 0 3.064 - 4.086: 0 4.086 - 5.107: 10 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CB DTH G 4 " pdb=" CA DTH G 4 " pdb=" OG1 DTH G 4 " pdb=" CG2 DTH G 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.56 5.11 2.00e-01 2.50e+01 6.52e+02 chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.11 2.00e-01 2.50e+01 6.52e+02 chirality pdb=" CB DTH I 4 " pdb=" CA DTH I 4 " pdb=" OG1 DTH I 4 " pdb=" CG2 DTH I 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.11 2.00e-01 2.50e+01 6.52e+02 ... (remaining 2302 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 375 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C PHE B 375 " -0.062 2.00e-02 2.50e+03 pdb=" O PHE B 375 " 0.022 2.00e-02 2.50e+03 pdb=" OXT PHE B 375 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 375 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C PHE E 375 " 0.062 2.00e-02 2.50e+03 pdb=" O PHE E 375 " -0.022 2.00e-02 2.50e+03 pdb=" OXT PHE E 375 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 375 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C PHE C 375 " 0.062 2.00e-02 2.50e+03 pdb=" O PHE C 375 " -0.022 2.00e-02 2.50e+03 pdb=" OXT PHE C 375 " -0.022 2.00e-02 2.50e+03 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 35 2.38 - 3.01: 9759 3.01 - 3.64: 21614 3.64 - 4.27: 36441 4.27 - 4.90: 58061 Nonbonded interactions: 125910 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP F 1 " pdb=" SG CYS F 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.752 3.620 nonbonded pdb=" CD1 TRP G 1 " pdb=" SG CYS G 5 " model vdw 1.753 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.753 3.620 ... (remaining 125905 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.290 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 : 0.017 0.100 15250 Z= 1.099 Angle : 1.607 10.897 20720 Z= 1.083 Chirality : 0.344 5.107 2305 Planarity : 0.006 0.060 2625 Dihedral : 12.357 149.759 5615 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.32 % Allowed : 0.00 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1830 helix: -1.01 (0.17), residues: 770 sheet: -0.88 (0.30), residues: 240 loop : -0.05 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 62 TYR 0.038 0.005 TYR D 294 PHE 0.021 0.004 PHE A 124 TRP 0.027 0.006 TRP B 340 HIS 0.008 0.002 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01742 / 1.10 (15240) covalent geometry : angle 1.60146 / 1.08 (20690) hydrogen bonds : bond 0.17274 / 11.83 ( 735) hydrogen bonds : angle 8.15669 / 5.61 ( 1815) link_TRANS : bond 0.00376 / 0.22 ( 10) link_TRANS : angle 3.71206 / 2.43 ( 30) *********************** 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 465 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 460 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.8209 (tp30) cc_final: 0.7930 (tp30) REVERT: A 370 VAL cc_start: 0.8452 (m) cc_final: 0.8140 (m) REVERT: C 78 ASN cc_start: 0.8592 (t0) cc_final: 0.8130 (t0) REVERT: C 157 ASP cc_start: 0.8345 (t70) cc_final: 0.8072 (t70) REVERT: C 187 ASP cc_start: 0.8366 (t70) cc_final: 0.8045 (t0) REVERT: C 305 MET cc_start: 0.8235 (mmm) cc_final: 0.7953 (mmt) REVERT: D 206 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7876 (ttm170) REVERT: E 40 HIS cc_start: 0.7922 (m-70) cc_final: 0.7641 (m-70) outliers start: 5 outliers final: 5 residues processed: 465 average time/residue: 0.1348 time to fit residues: 90.1843 Evaluate side-chains 232 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 227 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain G residue 5 CYS Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 162 ASN A 360 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN C 12 ASN C 173 HIS D 12 ASN D 40 HIS D 354 GLN E 173 HIS ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097049 restraints weight = 22439.702| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.12 r_work: 0.2999 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15250 Z= 0.168 Angle : 0.720 10.210 20720 Z= 0.358 Chirality : 0.050 0.396 2305 Planarity : 0.005 0.040 2625 Dihedral : 12.575 161.999 2125 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.84 % Allowed : 8.51 % Favored : 89.65 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1830 helix: 0.63 (0.19), residues: 730 sheet: -0.66 (0.28), residues: 320 loop : 0.78 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 372 TYR 0.012 0.001 TYR B 294 PHE 0.019 0.002 PHE C 375 TRP 0.018 0.002 TRP F 1 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (15240) covalent geometry : angle 0.71587 / 0.36 (20690) hydrogen bonds : bond 0.04383 / 3.01 ( 735) hydrogen bonds : angle 5.43875 / 3.79 ( 1815) link_TRANS : bond 0.00757 / 0.47 ( 10) link_TRANS : angle 2.21475 / 1.21 ( 30) *********************** 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 305 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 THR cc_start: 0.8961 (m) cc_final: 0.8373 (p) REVERT: A 227 MET cc_start: 0.8221 (mmm) cc_final: 0.7979 (tpp) REVERT: A 259 GLU cc_start: 0.8679 (tp30) cc_final: 0.8422 (tp30) REVERT: A 355 MET cc_start: 0.6179 (mtt) cc_final: 0.5856 (mmm) REVERT: B 118 LYS cc_start: 0.8868 (tppt) cc_final: 0.8600 (tttt) REVERT: B 211 ASP cc_start: 0.8770 (t70) cc_final: 0.8008 (m-30) REVERT: B 238 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8270 (mmmm) REVERT: B 271 SER cc_start: 0.8599 (m) cc_final: 0.8265 (p) REVERT: B 284 LYS cc_start: 0.8088 (mttt) cc_final: 0.7784 (mtpt) REVERT: B 285 CYS cc_start: 0.8430 (m) cc_final: 0.8167 (m) REVERT: C 44 MET cc_start: 0.8004 (mtt) cc_final: 0.7780 (mtt) REVERT: C 119 MET cc_start: 0.8153 (ttp) cc_final: 0.7784 (ttp) REVERT: C 187 ASP cc_start: 0.8822 (t70) cc_final: 0.8597 (t0) REVERT: C 276 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: C 286 ASP cc_start: 0.7885 (t0) cc_final: 0.7634 (m-30) REVERT: C 289 ILE cc_start: 0.8368 (mt) cc_final: 0.8131 (tt) REVERT: C 314 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8062 (tm-30) REVERT: D 123 MET cc_start: 0.8015 (mmt) cc_final: 0.7642 (mmt) REVERT: D 191 LYS cc_start: 0.8181 (tttt) cc_final: 0.7877 (ttmm) REVERT: D 206 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7742 (ttm170) REVERT: D 316 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7853 (mm-30) REVERT: E 40 HIS cc_start: 0.8369 (m-70) cc_final: 0.7987 (m-70) REVERT: E 44 MET cc_start: 0.1870 (tpt) cc_final: 0.1391 (mtp) REVERT: E 53 TYR cc_start: 0.8783 (m-80) cc_final: 0.8479 (m-80) REVERT: E 59 GLN cc_start: 0.8509 (tt0) cc_final: 0.8204 (mm-40) REVERT: E 191 LYS cc_start: 0.8823 (tttt) cc_final: 0.8521 (ttmt) REVERT: E 333 PRO cc_start: 0.7743 (Cg_exo) cc_final: 0.7481 (Cg_endo) outliers start: 29 outliers final: 17 residues processed: 295 average time/residue: 0.1204 time to fit residues: 53.4297 Evaluate side-chains 232 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 205 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 163 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS D 12 ASN D 40 HIS D 173 HIS D 353 GLN ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.086840 restraints weight = 22733.314| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.31 r_work: 0.2813 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15250 Z= 0.295 Angle : 0.743 7.874 20720 Z= 0.370 Chirality : 0.054 0.481 2305 Planarity : 0.005 0.045 2625 Dihedral : 12.082 175.155 2120 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.41 % Allowed : 10.10 % Favored : 87.49 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1830 helix: 0.52 (0.19), residues: 760 sheet: -0.64 (0.28), residues: 315 loop : 0.86 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 290 TYR 0.016 0.002 TYR D 143 PHE 0.016 0.002 PHE D 352 TRP 0.014 0.002 TRP D 340 HIS 0.005 0.002 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.29 (15240) covalent geometry : angle 0.74169 / 0.37 (20690) hydrogen bonds : bond 0.04576 / 3.11 ( 735) hydrogen bonds : angle 5.12637 / 3.56 ( 1815) link_TRANS : bond 0.00243 / 0.14 ( 10) link_TRANS : angle 1.37293 / 0.74 ( 30) *********************** 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 265 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 194 THR cc_start: 0.9115 (m) cc_final: 0.8556 (p) REVERT: A 227 MET cc_start: 0.8227 (mmm) cc_final: 0.7873 (tpp) REVERT: A 270 GLU cc_start: 0.5404 (mm-30) cc_final: 0.5049 (mm-30) REVERT: B 59 GLN cc_start: 0.8123 (tt0) cc_final: 0.7869 (tp40) REVERT: B 118 LYS cc_start: 0.8922 (tppt) cc_final: 0.8555 (tttt) REVERT: B 211 ASP cc_start: 0.8742 (t70) cc_final: 0.7908 (m-30) REVERT: B 227 MET cc_start: 0.8193 (mmt) cc_final: 0.7972 (mmt) REVERT: B 238 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8156 (mmmm) REVERT: B 271 SER cc_start: 0.8702 (m) cc_final: 0.8404 (p) REVERT: B 284 LYS cc_start: 0.8330 (mttt) cc_final: 0.8064 (mtpp) REVERT: B 285 CYS cc_start: 0.8740 (m) cc_final: 0.8432 (m) REVERT: B 296 ASN cc_start: 0.8694 (m-40) cc_final: 0.8326 (m110) REVERT: C 44 MET cc_start: 0.7938 (mtt) cc_final: 0.7662 (mtt) REVERT: C 82 MET cc_start: 0.8449 (tpt) cc_final: 0.7646 (tpt) REVERT: C 83 GLU cc_start: 0.8676 (tt0) cc_final: 0.8427 (mt-10) REVERT: C 117 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7582 (tm-30) REVERT: C 119 MET cc_start: 0.8204 (ttp) cc_final: 0.7940 (ttp) REVERT: C 276 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: C 286 ASP cc_start: 0.7961 (t0) cc_final: 0.7645 (m-30) REVERT: C 289 ILE cc_start: 0.8368 (mt) cc_final: 0.8097 (tt) REVERT: D 205 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: D 206 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7584 (ttm170) REVERT: D 316 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7941 (mm-30) REVERT: E 40 HIS cc_start: 0.8551 (m-70) cc_final: 0.8124 (m-70) REVERT: E 44 MET cc_start: 0.2213 (tpt) cc_final: 0.1894 (ttt) REVERT: E 59 GLN cc_start: 0.8622 (tt0) cc_final: 0.8264 (mm-40) REVERT: E 92 ASN cc_start: 0.7977 (m-40) cc_final: 0.7310 (t0) REVERT: E 125 GLU cc_start: 0.8129 (tp30) cc_final: 0.7811 (tp30) REVERT: E 143 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8247 (t80) REVERT: E 333 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7832 (Cg_endo) outliers start: 38 outliers final: 24 residues processed: 251 average time/residue: 0.1168 time to fit residues: 44.0748 Evaluate side-chains 223 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN D 12 ASN D 40 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.089505 restraints weight = 22243.969| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.30 r_work: 0.2853 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15250 Z= 0.159 Angle : 0.637 7.098 20720 Z= 0.309 Chirality : 0.050 0.472 2305 Planarity : 0.005 0.043 2625 Dihedral : 11.486 177.047 2120 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.10 % Allowed : 11.43 % Favored : 86.48 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1830 helix: 0.95 (0.19), residues: 730 sheet: -0.55 (0.28), residues: 315 loop : 0.81 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 95 TYR 0.009 0.001 TYR D 294 PHE 0.013 0.001 PHE A 31 TRP 0.011 0.002 TRP E 340 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15240) covalent geometry : angle 0.63542 / 0.31 (20690) hydrogen bonds : bond 0.03552 / 2.41 ( 735) hydrogen bonds : angle 4.80734 / 3.33 ( 1815) link_TRANS : bond 0.00307 / 0.19 ( 10) link_TRANS : angle 1.46621 / 0.77 ( 30) *********************** 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 265 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 95 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7959 (mtm-85) REVERT: A 176 MET cc_start: 0.8774 (mtp) cc_final: 0.8346 (mtt) REVERT: A 194 THR cc_start: 0.9134 (m) cc_final: 0.8597 (p) REVERT: A 227 MET cc_start: 0.8194 (mmm) cc_final: 0.7774 (tpp) REVERT: A 270 GLU cc_start: 0.5481 (mm-30) cc_final: 0.5105 (mm-30) REVERT: A 355 MET cc_start: 0.6015 (mtt) cc_final: 0.5677 (mmt) REVERT: B 118 LYS cc_start: 0.8943 (tppt) cc_final: 0.8539 (tttt) REVERT: B 211 ASP cc_start: 0.8737 (t70) cc_final: 0.7920 (m-30) REVERT: B 222 ASP cc_start: 0.8856 (t0) cc_final: 0.8581 (t0) REVERT: B 238 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8157 (mmmm) REVERT: B 271 SER cc_start: 0.8649 (m) cc_final: 0.8396 (p) REVERT: B 284 LYS cc_start: 0.8335 (mttt) cc_final: 0.8083 (tttm) REVERT: B 285 CYS cc_start: 0.8736 (m) cc_final: 0.8487 (m) REVERT: B 296 ASN cc_start: 0.8656 (m-40) cc_final: 0.8254 (m110) REVERT: B 314 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: C 190 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8796 (mtm) REVERT: C 276 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: C 286 ASP cc_start: 0.7911 (t0) cc_final: 0.7566 (m-30) REVERT: C 289 ILE cc_start: 0.8325 (mt) cc_final: 0.8090 (tt) REVERT: D 44 MET cc_start: 0.3079 (ttt) cc_final: 0.2649 (ttt) REVERT: D 121 GLN cc_start: 0.8181 (tt0) cc_final: 0.7955 (tm-30) REVERT: D 191 LYS cc_start: 0.8270 (tttt) cc_final: 0.7733 (ttmm) REVERT: D 205 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: D 206 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7506 (ttm170) REVERT: D 316 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7890 (mm-30) REVERT: E 40 HIS cc_start: 0.8542 (m-70) cc_final: 0.8146 (m-70) REVERT: E 59 GLN cc_start: 0.8676 (tt0) cc_final: 0.8423 (mm-40) REVERT: E 92 ASN cc_start: 0.8010 (m-40) cc_final: 0.7335 (t0) REVERT: E 139 VAL cc_start: 0.8978 (t) cc_final: 0.8729 (m) REVERT: E 143 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8307 (t80) REVERT: E 237 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: E 333 PRO cc_start: 0.8089 (Cg_exo) cc_final: 0.7842 (Cg_endo) REVERT: E 372 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.7050 (mtm110) outliers start: 33 outliers final: 24 residues processed: 253 average time/residue: 0.1119 time to fit residues: 42.8354 Evaluate side-chains 226 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 65 optimal weight: 0.0010 chunk 178 optimal weight: 2.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 40 HIS D 353 GLN D 354 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.086430 restraints weight = 22714.943| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.34 r_work: 0.2835 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15250 Z= 0.212 Angle : 0.655 7.319 20720 Z= 0.318 Chirality : 0.051 0.454 2305 Planarity : 0.005 0.040 2625 Dihedral : 11.142 174.632 2120 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.60 % Allowed : 12.83 % Favored : 84.57 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1830 helix: 0.98 (0.19), residues: 730 sheet: -0.59 (0.28), residues: 320 loop : 0.86 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 312 TYR 0.011 0.001 TYR D 143 PHE 0.013 0.002 PHE A 31 TRP 0.011 0.002 TRP E 340 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (15240) covalent geometry : angle 0.65348 / 0.32 (20690) hydrogen bonds : bond 0.03730 / 2.52 ( 735) hydrogen bonds : angle 4.77063 / 3.31 ( 1815) link_TRANS : bond 0.00236 / 0.14 ( 10) link_TRANS : angle 1.41465 / 0.75 ( 30) *********************** 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 251 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 194 THR cc_start: 0.9133 (m) cc_final: 0.8751 (p) REVERT: A 227 MET cc_start: 0.8204 (mmm) cc_final: 0.7758 (tpp) REVERT: A 270 GLU cc_start: 0.5572 (mm-30) cc_final: 0.5287 (mm-30) REVERT: A 355 MET cc_start: 0.6271 (mtt) cc_final: 0.5903 (mmt) REVERT: B 44 MET cc_start: 0.7881 (mtt) cc_final: 0.7568 (mtt) REVERT: B 118 LYS cc_start: 0.8951 (tppt) cc_final: 0.8545 (tttt) REVERT: B 211 ASP cc_start: 0.8726 (t70) cc_final: 0.7935 (m-30) REVERT: B 238 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8144 (mmmm) REVERT: B 271 SER cc_start: 0.8677 (m) cc_final: 0.8405 (p) REVERT: B 284 LYS cc_start: 0.8384 (mttt) cc_final: 0.8085 (tttm) REVERT: B 285 CYS cc_start: 0.8741 (m) cc_final: 0.8434 (m) REVERT: B 296 ASN cc_start: 0.8696 (m-40) cc_final: 0.8332 (m110) REVERT: B 314 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: C 44 MET cc_start: 0.8351 (mtt) cc_final: 0.8138 (mtt) REVERT: C 82 MET cc_start: 0.8374 (tpt) cc_final: 0.7640 (tpt) REVERT: C 118 LYS cc_start: 0.8807 (tppt) cc_final: 0.8277 (mtpt) REVERT: C 190 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8815 (mtm) REVERT: C 276 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: C 286 ASP cc_start: 0.7936 (t0) cc_final: 0.7649 (m-30) REVERT: C 289 ILE cc_start: 0.8355 (mt) cc_final: 0.8103 (tt) REVERT: D 44 MET cc_start: 0.3120 (ttt) cc_final: 0.2415 (ttt) REVERT: D 191 LYS cc_start: 0.8277 (tttt) cc_final: 0.7763 (ttmm) REVERT: D 205 GLU cc_start: 0.8618 (mp0) cc_final: 0.8205 (mp0) REVERT: D 206 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7545 (ttm170) REVERT: D 316 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7957 (mm-30) REVERT: E 59 GLN cc_start: 0.8701 (tt0) cc_final: 0.8402 (mm-40) REVERT: E 92 ASN cc_start: 0.8015 (m-40) cc_final: 0.7305 (t0) REVERT: E 139 VAL cc_start: 0.9008 (t) cc_final: 0.8766 (m) REVERT: E 143 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.8267 (t80) REVERT: E 237 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: E 314 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: E 333 PRO cc_start: 0.8182 (Cg_exo) cc_final: 0.7947 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8633 (pt0) cc_final: 0.8182 (pp30) REVERT: E 372 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.7164 (mtm110) outliers start: 41 outliers final: 28 residues processed: 238 average time/residue: 0.1177 time to fit residues: 42.2190 Evaluate side-chains 225 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 88 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.092783 restraints weight = 21845.812| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.27 r_work: 0.2882 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15250 Z= 0.114 Angle : 0.600 6.605 20720 Z= 0.286 Chirality : 0.048 0.404 2305 Planarity : 0.004 0.041 2625 Dihedral : 10.666 178.041 2120 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.10 % Allowed : 13.59 % Favored : 84.32 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1830 helix: 1.22 (0.19), residues: 730 sheet: -0.41 (0.28), residues: 315 loop : 0.91 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 95 TYR 0.007 0.001 TYR E 362 PHE 0.015 0.001 PHE C 124 TRP 0.009 0.001 TRP E 340 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15240) covalent geometry : angle 0.59835 / 0.29 (20690) hydrogen bonds : bond 0.03076 / 2.10 ( 735) hydrogen bonds : angle 4.60781 / 3.20 ( 1815) link_TRANS : bond 0.00307 / 0.20 ( 10) link_TRANS : angle 1.34449 / 0.71 ( 30) *********************** 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 246 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7181 (mtt) cc_final: 0.6682 (mmm) REVERT: A 83 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 194 THR cc_start: 0.9170 (m) cc_final: 0.8693 (p) REVERT: A 270 GLU cc_start: 0.5564 (mm-30) cc_final: 0.5205 (mm-30) REVERT: A 355 MET cc_start: 0.6178 (mtt) cc_final: 0.5870 (mmt) REVERT: B 118 LYS cc_start: 0.8963 (tppt) cc_final: 0.8529 (tttt) REVERT: B 132 MET cc_start: 0.7512 (ptt) cc_final: 0.7285 (ptm) REVERT: B 238 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8136 (mmmm) REVERT: B 284 LYS cc_start: 0.8288 (mttt) cc_final: 0.8058 (tttm) REVERT: B 285 CYS cc_start: 0.8708 (m) cc_final: 0.8280 (m) REVERT: B 314 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: B 354 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: C 44 MET cc_start: 0.7948 (mtt) cc_final: 0.7604 (mtt) REVERT: C 47 MET cc_start: 0.6662 (mtp) cc_final: 0.6371 (mtp) REVERT: C 82 MET cc_start: 0.8382 (tpt) cc_final: 0.7611 (tpt) REVERT: C 118 LYS cc_start: 0.8827 (tppt) cc_final: 0.8336 (mtpt) REVERT: C 187 ASP cc_start: 0.8795 (t0) cc_final: 0.8486 (m-30) REVERT: C 190 MET cc_start: 0.8967 (ttp) cc_final: 0.8728 (mtm) REVERT: C 276 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: D 44 MET cc_start: 0.3162 (ttt) cc_final: 0.2402 (ttt) REVERT: D 191 LYS cc_start: 0.8377 (tttt) cc_final: 0.7872 (ttmm) REVERT: D 205 GLU cc_start: 0.8506 (mp0) cc_final: 0.8108 (mp0) REVERT: D 206 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7481 (ttm170) REVERT: D 227 MET cc_start: 0.8371 (mmm) cc_final: 0.8097 (mmm) REVERT: D 316 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7861 (mm-30) REVERT: D 355 MET cc_start: 0.8377 (mtp) cc_final: 0.8158 (mtt) REVERT: E 59 GLN cc_start: 0.8674 (tt0) cc_final: 0.8368 (mm-40) REVERT: E 92 ASN cc_start: 0.8038 (m-40) cc_final: 0.7343 (t0) REVERT: E 139 VAL cc_start: 0.9025 (t) cc_final: 0.8802 (m) REVERT: E 143 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8378 (t80) REVERT: E 237 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: E 314 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: E 333 PRO cc_start: 0.8062 (Cg_exo) cc_final: 0.7830 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8580 (pt0) cc_final: 0.8176 (pp30) outliers start: 33 outliers final: 22 residues processed: 238 average time/residue: 0.1134 time to fit residues: 40.9830 Evaluate side-chains 222 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 154 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 40 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.087927 restraints weight = 22360.546| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.33 r_work: 0.2875 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15250 Z= 0.143 Angle : 0.606 6.954 20720 Z= 0.288 Chirality : 0.048 0.396 2305 Planarity : 0.004 0.038 2625 Dihedral : 10.400 172.577 2120 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.48 % Allowed : 13.71 % Favored : 83.81 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1830 helix: 1.31 (0.19), residues: 730 sheet: -0.40 (0.28), residues: 330 loop : 1.05 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.009 0.001 TYR D 143 PHE 0.015 0.001 PHE C 124 TRP 0.009 0.001 TRP A 86 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (15240) covalent geometry : angle 0.60454 / 0.29 (20690) hydrogen bonds : bond 0.03199 / 2.16 ( 735) hydrogen bonds : angle 4.54184 / 3.15 ( 1815) link_TRANS : bond 0.00242 / 0.16 ( 10) link_TRANS : angle 1.27222 / 0.68 ( 30) *********************** 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 238 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 194 THR cc_start: 0.9149 (m) cc_final: 0.8781 (p) REVERT: A 227 MET cc_start: 0.8461 (tpp) cc_final: 0.7841 (mpp) REVERT: A 270 GLU cc_start: 0.5325 (mm-30) cc_final: 0.4647 (mm-30) REVERT: A 355 MET cc_start: 0.6394 (mtt) cc_final: 0.6004 (mmm) REVERT: B 118 LYS cc_start: 0.8945 (tppt) cc_final: 0.8492 (tttt) REVERT: B 238 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8095 (mmmm) REVERT: B 284 LYS cc_start: 0.8276 (mttt) cc_final: 0.8015 (tttm) REVERT: B 296 ASN cc_start: 0.8701 (m-40) cc_final: 0.8405 (m-40) REVERT: B 314 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: C 44 MET cc_start: 0.8153 (mtt) cc_final: 0.7742 (mtt) REVERT: C 47 MET cc_start: 0.6821 (mtp) cc_final: 0.6313 (mtp) REVERT: C 82 MET cc_start: 0.8362 (tpt) cc_final: 0.7598 (tpt) REVERT: C 187 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: C 190 MET cc_start: 0.8992 (ttp) cc_final: 0.8745 (mtm) REVERT: C 276 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: C 333 PRO cc_start: 0.8285 (Cg_exo) cc_final: 0.8081 (Cg_endo) REVERT: D 191 LYS cc_start: 0.8287 (tttt) cc_final: 0.7669 (ttmt) REVERT: D 205 GLU cc_start: 0.8574 (mp0) cc_final: 0.8154 (mp0) REVERT: D 206 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7486 (ttm170) REVERT: D 316 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7868 (mm-30) REVERT: D 355 MET cc_start: 0.8360 (mtp) cc_final: 0.8089 (mtp) REVERT: E 44 MET cc_start: 0.3371 (ttt) cc_final: 0.3150 (ttt) REVERT: E 59 GLN cc_start: 0.8677 (tt0) cc_final: 0.8323 (mm-40) REVERT: E 92 ASN cc_start: 0.8030 (m-40) cc_final: 0.7278 (t0) REVERT: E 132 MET cc_start: 0.8657 (ttt) cc_final: 0.8450 (ttt) REVERT: E 139 VAL cc_start: 0.9029 (t) cc_final: 0.8817 (m) REVERT: E 143 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8390 (t80) REVERT: E 237 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: E 314 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: E 324 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8736 (t) REVERT: E 333 PRO cc_start: 0.8134 (Cg_exo) cc_final: 0.7904 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8657 (pt0) cc_final: 0.8195 (pp30) REVERT: E 375 PHE cc_start: 0.4195 (OUTLIER) cc_final: 0.3752 (m-80) outliers start: 39 outliers final: 22 residues processed: 226 average time/residue: 0.1191 time to fit residues: 40.6243 Evaluate side-chains 214 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 131 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.090256 restraints weight = 22488.573| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.22 r_work: 0.2836 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15250 Z= 0.193 Angle : 0.635 8.641 20720 Z= 0.305 Chirality : 0.048 0.397 2305 Planarity : 0.005 0.039 2625 Dihedral : 10.379 169.779 2120 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.41 % Allowed : 14.10 % Favored : 83.49 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1830 helix: 1.25 (0.19), residues: 730 sheet: -0.44 (0.29), residues: 320 loop : 0.88 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.010 0.001 TYR D 143 PHE 0.015 0.001 PHE C 124 TRP 0.012 0.002 TRP A 86 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (15240) covalent geometry : angle 0.63423 / 0.30 (20690) hydrogen bonds : bond 0.03480 / 2.34 ( 735) hydrogen bonds : angle 4.62626 / 3.20 ( 1815) link_TRANS : bond 0.00204 / 0.14 ( 10) link_TRANS : angle 1.20530 / 0.64 ( 30) *********************** 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 229 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7006 (mtt) cc_final: 0.6805 (mmm) REVERT: A 83 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 194 THR cc_start: 0.9209 (m) cc_final: 0.8844 (p) REVERT: A 269 MET cc_start: 0.8646 (mtt) cc_final: 0.8344 (mtp) REVERT: A 270 GLU cc_start: 0.5508 (mm-30) cc_final: 0.4835 (mm-30) REVERT: A 355 MET cc_start: 0.6578 (mtt) cc_final: 0.6354 (mtt) REVERT: B 118 LYS cc_start: 0.8961 (tppt) cc_final: 0.8554 (tttt) REVERT: B 238 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8129 (mmmm) REVERT: B 283 MET cc_start: 0.8316 (mmm) cc_final: 0.8043 (mmt) REVERT: B 284 LYS cc_start: 0.8401 (mttt) cc_final: 0.8167 (tttm) REVERT: B 296 ASN cc_start: 0.8628 (m-40) cc_final: 0.8304 (m-40) REVERT: B 314 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: C 44 MET cc_start: 0.8008 (mtt) cc_final: 0.7629 (mtt) REVERT: C 47 MET cc_start: 0.6574 (mtp) cc_final: 0.6150 (mtp) REVERT: C 82 MET cc_start: 0.8417 (tpt) cc_final: 0.7754 (tpt) REVERT: C 117 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7538 (tm-30) REVERT: C 118 LYS cc_start: 0.8822 (tppt) cc_final: 0.8508 (tptm) REVERT: C 187 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8478 (m-30) REVERT: C 190 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8785 (mtm) REVERT: C 276 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 289 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8118 (tt) REVERT: D 191 LYS cc_start: 0.8350 (tttt) cc_final: 0.7779 (ttmm) REVERT: D 205 GLU cc_start: 0.8602 (mp0) cc_final: 0.8263 (mp0) REVERT: D 206 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7558 (ttm170) REVERT: D 316 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7857 (mm-30) REVERT: E 44 MET cc_start: 0.3640 (ttt) cc_final: 0.3394 (ttt) REVERT: E 92 ASN cc_start: 0.8038 (m-40) cc_final: 0.7437 (t0) REVERT: E 132 MET cc_start: 0.8675 (ttt) cc_final: 0.8473 (ttt) REVERT: E 139 VAL cc_start: 0.9077 (t) cc_final: 0.8868 (m) REVERT: E 143 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8402 (t80) REVERT: E 237 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: E 314 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: E 324 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8756 (t) REVERT: E 333 PRO cc_start: 0.8130 (Cg_exo) cc_final: 0.7912 (Cg_endo) REVERT: E 375 PHE cc_start: 0.4134 (OUTLIER) cc_final: 0.3645 (m-80) outliers start: 38 outliers final: 24 residues processed: 214 average time/residue: 0.1072 time to fit residues: 35.7764 Evaluate side-chains 219 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.088083 restraints weight = 22674.843| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.24 r_work: 0.2861 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15250 Z= 0.182 Angle : 0.633 9.101 20720 Z= 0.303 Chirality : 0.048 0.388 2305 Planarity : 0.004 0.039 2625 Dihedral : 10.140 160.729 2120 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.41 % Allowed : 14.22 % Favored : 83.37 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1830 helix: 1.25 (0.19), residues: 730 sheet: -0.36 (0.29), residues: 315 loop : 0.83 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.010 0.001 TYR D 143 PHE 0.014 0.001 PHE C 124 TRP 0.010 0.002 TRP C 79 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (15240) covalent geometry : angle 0.63222 / 0.30 (20690) hydrogen bonds : bond 0.03406 / 2.30 ( 735) hydrogen bonds : angle 4.60086 / 3.18 ( 1815) link_TRANS : bond 0.00166 / 0.10 ( 10) link_TRANS : angle 1.18891 / 0.64 ( 30) *********************** 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 224 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7135 (mtt) cc_final: 0.6870 (mmm) REVERT: A 83 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 194 THR cc_start: 0.9200 (m) cc_final: 0.8840 (p) REVERT: A 227 MET cc_start: 0.8466 (tpp) cc_final: 0.8160 (tpp) REVERT: A 269 MET cc_start: 0.8635 (mtt) cc_final: 0.8311 (mtp) REVERT: A 270 GLU cc_start: 0.5635 (mm-30) cc_final: 0.4912 (mm-30) REVERT: A 355 MET cc_start: 0.6520 (mtt) cc_final: 0.6319 (mtt) REVERT: B 118 LYS cc_start: 0.8971 (tppt) cc_final: 0.8565 (tttt) REVERT: B 238 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8107 (mmmm) REVERT: B 284 LYS cc_start: 0.8331 (mttt) cc_final: 0.8098 (tttm) REVERT: B 296 ASN cc_start: 0.8602 (m-40) cc_final: 0.8254 (m-40) REVERT: B 314 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: C 82 MET cc_start: 0.8393 (tpt) cc_final: 0.7733 (tpt) REVERT: C 117 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7513 (tm-30) REVERT: C 118 LYS cc_start: 0.8818 (tppt) cc_final: 0.8484 (tptm) REVERT: C 187 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: C 190 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8780 (mtm) REVERT: C 276 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 289 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8108 (tt) REVERT: D 44 MET cc_start: 0.3261 (ttt) cc_final: 0.2958 (ttt) REVERT: D 191 LYS cc_start: 0.8354 (tttt) cc_final: 0.7809 (ttmm) REVERT: D 206 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7546 (ttm170) REVERT: D 227 MET cc_start: 0.8419 (mmm) cc_final: 0.8080 (mmm) REVERT: D 316 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7832 (mm-30) REVERT: E 92 ASN cc_start: 0.8025 (m-40) cc_final: 0.7369 (t0) REVERT: E 132 MET cc_start: 0.8681 (ttt) cc_final: 0.8464 (ttt) REVERT: E 139 VAL cc_start: 0.9076 (t) cc_final: 0.8858 (m) REVERT: E 143 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.8421 (t80) REVERT: E 237 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: E 314 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: E 333 PRO cc_start: 0.7976 (Cg_exo) cc_final: 0.7744 (Cg_endo) REVERT: E 375 PHE cc_start: 0.4301 (OUTLIER) cc_final: 0.3625 (m-80) outliers start: 38 outliers final: 25 residues processed: 208 average time/residue: 0.1079 time to fit residues: 34.7004 Evaluate side-chains 214 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 176 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 121 optimal weight: 0.2980 chunk 168 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 HIS B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.088487 restraints weight = 22319.166| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.22 r_work: 0.2866 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 15250 Z= 0.179 Angle : 0.839 59.200 20720 Z= 0.448 Chirality : 0.047 0.381 2305 Planarity : 0.005 0.072 2625 Dihedral : 10.164 160.382 2120 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 2.22 % Allowed : 14.03 % Favored : 83.75 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1830 helix: 1.29 (0.19), residues: 730 sheet: -0.36 (0.29), residues: 315 loop : 0.83 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 95 TYR 0.009 0.001 TYR D 143 PHE 0.047 0.002 PHE E 375 TRP 0.013 0.002 TRP D 86 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (15240) covalent geometry : angle 0.83848 / 0.45 (20690) hydrogen bonds : bond 0.03334 / 2.25 ( 735) hydrogen bonds : angle 4.60303 / 3.18 ( 1815) link_TRANS : bond 0.00234 / 0.16 ( 10) link_TRANS : angle 1.19218 / 0.64 ( 30) ********************** 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 218 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7148 (mtt) cc_final: 0.6878 (mmm) REVERT: A 83 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 194 THR cc_start: 0.9198 (m) cc_final: 0.8835 (p) REVERT: A 227 MET cc_start: 0.8483 (tpp) cc_final: 0.8181 (tpp) REVERT: A 269 MET cc_start: 0.8631 (mtt) cc_final: 0.8304 (mtp) REVERT: A 270 GLU cc_start: 0.5617 (mm-30) cc_final: 0.4949 (mm-30) REVERT: A 355 MET cc_start: 0.6514 (mtt) cc_final: 0.6312 (mtt) REVERT: B 118 LYS cc_start: 0.8969 (tppt) cc_final: 0.8565 (tttt) REVERT: B 238 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8104 (mmmm) REVERT: B 284 LYS cc_start: 0.8306 (mttt) cc_final: 0.8091 (tttm) REVERT: B 296 ASN cc_start: 0.8577 (m-40) cc_final: 0.8226 (m-40) REVERT: B 314 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: C 82 MET cc_start: 0.8392 (tpt) cc_final: 0.7729 (tpt) REVERT: C 117 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7524 (tm-30) REVERT: C 118 LYS cc_start: 0.8814 (tppt) cc_final: 0.8485 (tptm) REVERT: C 187 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8441 (m-30) REVERT: C 190 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8775 (mtm) REVERT: C 276 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: C 289 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8102 (tt) REVERT: D 44 MET cc_start: 0.3288 (ttt) cc_final: 0.2932 (ttt) REVERT: D 191 LYS cc_start: 0.8361 (tttt) cc_final: 0.7816 (ttmm) REVERT: D 206 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7539 (ttm170) REVERT: D 227 MET cc_start: 0.8425 (mmm) cc_final: 0.8082 (mmm) REVERT: D 316 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7820 (mm-30) REVERT: E 92 ASN cc_start: 0.8036 (m-40) cc_final: 0.7380 (t0) REVERT: E 132 MET cc_start: 0.8648 (ttt) cc_final: 0.8437 (ttt) REVERT: E 139 VAL cc_start: 0.9070 (t) cc_final: 0.8855 (m) REVERT: E 143 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8406 (t80) REVERT: E 237 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: E 314 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: E 333 PRO cc_start: 0.7985 (Cg_exo) cc_final: 0.7762 (Cg_endo) outliers start: 35 outliers final: 24 residues processed: 203 average time/residue: 0.1127 time to fit residues: 34.9462 Evaluate side-chains 212 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 138 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 HIS B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.088815 restraints weight = 22462.812| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.23 r_work: 0.2879 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 15250 Z= 0.179 Angle : 0.839 59.200 20720 Z= 0.448 Chirality : 0.047 0.381 2305 Planarity : 0.005 0.072 2625 Dihedral : 10.164 160.382 2120 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 2.10 % Allowed : 14.16 % Favored : 83.75 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1830 helix: 1.29 (0.19), residues: 730 sheet: -0.36 (0.29), residues: 315 loop : 0.83 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 95 TYR 0.009 0.001 TYR D 143 PHE 0.047 0.002 PHE E 375 TRP 0.013 0.002 TRP D 86 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (15240) covalent geometry : angle 0.83848 / 0.45 (20690) hydrogen bonds : bond 0.03334 / 2.25 ( 735) hydrogen bonds : angle 4.60303 / 3.18 ( 1815) link_TRANS : bond 0.00234 / 0.16 ( 10) link_TRANS : angle 1.19218 / 0.64 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.63 seconds wall clock time: 54 minutes 4.21 seconds (3244.21 seconds total)