Starting phenix.real_space_refine on Thu Jun 4 19:58:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t1y_10363/06_2026/6t1y_10363.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t1y_10363/06_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 { model { file = "/net/cci-nas-00/data/ceres_data/6t1y_10363/06_2026/6t1y_10363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t1y_10363/06_2026/6t1y_10363.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t1y_10363/06_2026/6t1y_10363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t1y_10363/06_2026/6t1y_10363.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 3.74, per 1000 atoms: 0.25 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: 1.31 Conformation dependent library (CDL) restraints added in 549.9 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: 0.62 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: 2.87 Time building geometry restraints manager: 1.67 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=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" C HYP G 6 " pdb=" N ALA G 7 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" O3A ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sigma weight residual 1.610 1.532 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O3A ADP C 376 " pdb=" PA ADP C 376 " ideal model delta sigma weight residual 1.610 1.532 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O3A ADP B 376 " pdb=" PA ADP B 376 " ideal model delta sigma weight residual 1.610 1.532 0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 18740 2.50 - 5.01: 1669 5.01 - 7.51: 189 7.51 - 10.02: 82 10.02 - 12.52: 10 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: 9024 29.95 - 59.90: 106 59.90 - 89.86: 45 89.86 - 119.81: 0 119.81 - 149.76: 10 Dihedral angle restraints: 9185 sinusoidal: 3730 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 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 860 0.043 - 0.087: 760 0.087 - 0.130: 391 0.130 - 0.174: 221 0.174 - 0.217: 73 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA TYR B 91 " pdb=" N TYR B 91 " pdb=" C TYR B 91 " pdb=" CB TYR B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR D 91 " pdb=" N TYR D 91 " pdb=" C TYR D 91 " pdb=" CB TYR D 91 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA TYR C 91 " pdb=" N TYR C 91 " pdb=" C TYR C 91 " pdb=" CB TYR C 91 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 ... (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: 0.06 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.240 Find NCS groups from input model: 0.170 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 0.078 15250 Z= 1.095 Angle : 1.602 12.521 20720 Z= 1.082 Chirality : 0.082 0.217 2305 Planarity : 0.006 0.060 2625 Dihedral : 12.521 149.759 5665 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 0.01733 / 1.10 (15240) covalent geometry : angle 1.59686 / 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 : 0.547 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: 0.8129 (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: 0.7642 (m-70) outliers start: 5 outliers final: 5 residues processed: 465 average time/residue: 0.1302 time to fit residues: 86.5744 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 : 0.553 ------------------------------------------------------------------------------- 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: 0.8980 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: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 162 ASN A 360 GLN 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 = 0.3321 r_free = 0.3321 target = 0.114091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.097928 restraints weight = 22344.048| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.10 r_work: 0.3004 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15250 Z= 0.162 Angle : 0.692 8.578 20720 Z= 0.349 Chirality : 0.047 0.216 2305 Planarity : 0.005 0.040 2625 Dihedral : 12.807 163.154 2175 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.97 % Allowed : 8.51 % Favored : 89.52 % 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: 0.49 (0.20), residues: 1830 helix: 0.64 (0.19), residues: 730 sheet: -0.68 (0.27), residues: 320 loop : 0.75 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 95 TYR 0.012 0.001 TYR B 294 PHE 0.022 0.002 PHE D 352 TRP 0.016 0.002 TRP F 1 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (15240) covalent geometry : angle 0.69136 / 0.35 (20690) hydrogen bonds : bond 0.04312 / 2.96 ( 735) hydrogen bonds : angle 5.43802 / 3.79 ( 1815) link_TRANS : bond 0.00321 / 0.21 ( 10) link_TRANS : angle 1.01126 / 0.57 ( 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 311 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8811 (mtp) cc_final: 0.8453 (mtt) REVERT: A 227 MET cc_start: 0.8218 (mmm) cc_final: 0.7981 (tpp) REVERT: A 259 GLU cc_start: 0.8709 (tp30) cc_final: 0.8476 (tp30) REVERT: A 364 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8264 (mm-30) REVERT: B 118 LYS cc_start: 0.8864 (tppt) cc_final: 0.8559 (tttt) REVERT: B 211 ASP cc_start: 0.8795 (t70) cc_final: 0.8004 (m-30) REVERT: B 238 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8255 (mmmm) REVERT: B 271 SER cc_start: 0.8558 (m) cc_final: 0.8214 (p) REVERT: B 284 LYS cc_start: 0.8026 (mttt) cc_final: 0.7740 (mtpt) REVERT: B 285 CYS cc_start: 0.8435 (m) cc_final: 0.8167 (m) REVERT: C 44 MET cc_start: 0.7951 (mtt) cc_final: 0.7739 (mtt) REVERT: C 119 MET cc_start: 0.8197 (ttp) cc_final: 0.7907 (ttp) REVERT: C 187 ASP cc_start: 0.8808 (t70) cc_final: 0.8570 (t0) REVERT: C 276 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: C 286 ASP cc_start: 0.7852 (t0) cc_final: 0.7624 (m-30) REVERT: C 289 ILE cc_start: 0.8344 (mt) cc_final: 0.8110 (tt) REVERT: C 314 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8065 (tm-30) REVERT: D 47 MET cc_start: 0.5955 (mtp) cc_final: 0.5182 (ttm) REVERT: D 123 MET cc_start: 0.8003 (mmt) cc_final: 0.7651 (mmt) REVERT: D 191 LYS cc_start: 0.8158 (tttt) cc_final: 0.7873 (ttmm) REVERT: D 206 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7745 (ttm170) REVERT: D 316 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7864 (mm-30) REVERT: D 353 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7857 (mm110) REVERT: E 40 HIS cc_start: 0.8390 (m-70) cc_final: 0.8002 (m-70) REVERT: E 44 MET cc_start: 0.1887 (tpt) cc_final: 0.1328 (mtp) REVERT: E 59 GLN cc_start: 0.8509 (tt0) cc_final: 0.8211 (mm-40) REVERT: E 191 LYS cc_start: 0.8847 (tttt) cc_final: 0.8554 (ttmt) REVERT: E 326 LYS cc_start: 0.8643 (tppt) cc_final: 0.8438 (tppt) REVERT: E 333 PRO cc_start: 0.7640 (Cg_exo) cc_final: 0.7389 (Cg_endo) outliers start: 31 outliers final: 17 residues processed: 301 average time/residue: 0.1116 time to fit residues: 50.4478 Evaluate side-chains 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 364 GLU 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 178 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 338 SER 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: 3.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS D 12 ASN D 40 HIS D 173 HIS ** 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 = 0.3171 r_free = 0.3171 target = 0.103736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.086218 restraints weight = 22760.696| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.32 r_work: 0.2821 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15250 Z= 0.297 Angle : 0.738 7.315 20720 Z= 0.369 Chirality : 0.050 0.254 2305 Planarity : 0.005 0.050 2625 Dihedral : 12.120 174.738 2170 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.35 % Allowed : 10.48 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.54 (0.19), residues: 1830 helix: 0.70 (0.19), residues: 730 sheet: -0.65 (0.28), residues: 315 loop : 0.72 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 116 TYR 0.016 0.002 TYR D 143 PHE 0.019 0.003 PHE B 375 TRP 0.016 0.003 TRP D 340 HIS 0.006 0.002 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.30 (15240) covalent geometry : angle 0.73840 / 0.37 (20690) hydrogen bonds : bond 0.04667 / 3.15 ( 735) hydrogen bonds : angle 5.13103 / 3.56 ( 1815) link_TRANS : bond 0.00425 / 0.27 ( 10) link_TRANS : angle 0.70214 / 0.42 ( 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 268 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9022 (t) cc_final: 0.8819 (m) REVERT: A 83 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 227 MET cc_start: 0.8238 (mmm) cc_final: 0.7885 (tpp) REVERT: A 270 GLU cc_start: 0.5429 (mm-30) cc_final: 0.5044 (mm-30) REVERT: A 355 MET cc_start: 0.6018 (mtt) cc_final: 0.5712 (mmt) REVERT: B 59 GLN cc_start: 0.8140 (tt0) cc_final: 0.7926 (tp40) REVERT: B 118 LYS cc_start: 0.8942 (tppt) cc_final: 0.8570 (tttt) REVERT: B 211 ASP cc_start: 0.8717 (t70) cc_final: 0.7876 (m-30) REVERT: B 238 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8132 (mmmm) REVERT: B 271 SER cc_start: 0.8698 (m) cc_final: 0.8401 (p) REVERT: B 285 CYS cc_start: 0.8755 (m) cc_final: 0.8494 (m) REVERT: B 296 ASN cc_start: 0.8688 (m-40) cc_final: 0.8319 (m110) REVERT: C 82 MET cc_start: 0.8430 (tpt) cc_final: 0.7619 (tpt) REVERT: C 83 GLU cc_start: 0.8689 (tt0) cc_final: 0.8388 (mt-10) REVERT: C 117 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7549 (tm-30) REVERT: C 119 MET cc_start: 0.8190 (ttp) cc_final: 0.7936 (ttp) REVERT: C 276 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: C 286 ASP cc_start: 0.7952 (t0) cc_final: 0.7650 (m-30) REVERT: C 289 ILE cc_start: 0.8355 (mt) cc_final: 0.8103 (tt) REVERT: C 353 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7965 (mm-40) REVERT: D 205 GLU cc_start: 0.8611 (mp0) cc_final: 0.8180 (mp0) REVERT: D 206 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7600 (ttm170) REVERT: D 316 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7916 (mm-30) REVERT: E 40 HIS cc_start: 0.8558 (m-70) cc_final: 0.8125 (m-70) REVERT: E 44 MET cc_start: 0.2211 (tpt) cc_final: 0.1770 (ttt) REVERT: E 59 GLN cc_start: 0.8651 (tt0) cc_final: 0.8272 (mm-40) REVERT: E 78 ASN cc_start: 0.8276 (t0) cc_final: 0.7833 (t0) REVERT: E 107 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8299 (tp30) REVERT: E 125 GLU cc_start: 0.8109 (tp30) cc_final: 0.7791 (tp30) REVERT: E 143 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8298 (t80) REVERT: E 326 LYS cc_start: 0.8738 (tppt) cc_final: 0.8538 (tppt) REVERT: E 333 PRO cc_start: 0.8091 (Cg_exo) cc_final: 0.7832 (Cg_endo) outliers start: 37 outliers final: 24 residues processed: 255 average time/residue: 0.1109 time to fit residues: 42.4475 Evaluate side-chains 224 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 349 LEU 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 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 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 129 VAL 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: 0.7980 chunk 41 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 40 HIS E 12 ASN ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.089247 restraints weight = 22255.237| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.32 r_work: 0.2850 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3852 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= 0.142 Angle : 0.610 6.761 20720 Z= 0.295 Chirality : 0.045 0.234 2305 Planarity : 0.005 0.043 2625 Dihedral : 11.417 178.926 2170 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.97 % Allowed : 12.57 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.20), residues: 1830 helix: 1.05 (0.19), residues: 730 sheet: -0.62 (0.28), residues: 320 loop : 0.88 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 95 TYR 0.012 0.001 TYR E 53 PHE 0.018 0.001 PHE B 375 TRP 0.010 0.002 TRP E 340 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (15240) covalent geometry : angle 0.61060 / 0.29 (20690) hydrogen bonds : bond 0.03384 / 2.30 ( 735) hydrogen bonds : angle 4.76170 / 3.31 ( 1815) link_TRANS : bond 0.00185 / 0.12 ( 10) link_TRANS : angle 0.48231 / 0.28 ( 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 263 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.566 Fit side-chains REVERT: A 83 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 95 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7991 (mtm-85) REVERT: A 227 MET cc_start: 0.8170 (mmm) cc_final: 0.7730 (tpp) REVERT: A 270 GLU cc_start: 0.5488 (mm-30) cc_final: 0.5098 (mm-30) REVERT: A 355 MET cc_start: 0.5834 (mtt) cc_final: 0.5560 (mmm) REVERT: B 118 LYS cc_start: 0.8949 (tppt) cc_final: 0.8530 (tttt) REVERT: B 211 ASP cc_start: 0.8734 (t70) cc_final: 0.7917 (m-30) REVERT: B 222 ASP cc_start: 0.8855 (t0) cc_final: 0.8605 (t0) REVERT: B 238 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8148 (mmmm) REVERT: B 271 SER cc_start: 0.8645 (m) cc_final: 0.8388 (p) REVERT: B 284 LYS cc_start: 0.8353 (mttt) cc_final: 0.8088 (tttm) REVERT: B 285 CYS cc_start: 0.8745 (m) cc_final: 0.8482 (m) REVERT: B 296 ASN cc_start: 0.8660 (m-40) cc_final: 0.8254 (m110) REVERT: B 314 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: C 118 LYS cc_start: 0.8786 (tppt) cc_final: 0.8241 (mtpt) REVERT: C 190 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8786 (mtm) REVERT: C 276 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: D 44 MET cc_start: 0.3046 (ttt) cc_final: 0.2640 (ttt) REVERT: D 72 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8228 (mt-10) REVERT: D 191 LYS cc_start: 0.8395 (tttt) cc_final: 0.7690 (ttmm) REVERT: D 205 GLU cc_start: 0.8539 (mp0) cc_final: 0.8096 (mp0) REVERT: D 206 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7480 (ttm170) REVERT: D 316 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7939 (mm-30) REVERT: E 40 HIS cc_start: 0.8539 (m-70) cc_final: 0.8143 (m-70) REVERT: E 59 GLN cc_start: 0.8650 (tt0) cc_final: 0.8377 (mm-40) REVERT: E 78 ASN cc_start: 0.8034 (t0) cc_final: 0.7814 (t0) REVERT: E 92 ASN cc_start: 0.8017 (m-40) cc_final: 0.7293 (t0) REVERT: E 139 VAL cc_start: 0.8972 (t) cc_final: 0.8732 (m) REVERT: E 143 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8305 (t80) REVERT: E 237 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: E 333 PRO cc_start: 0.7981 (Cg_exo) cc_final: 0.7740 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8599 (pt0) cc_final: 0.8207 (pp30) outliers start: 31 outliers final: 19 residues processed: 252 average time/residue: 0.1120 time to fit residues: 42.3105 Evaluate side-chains 230 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 143 TYR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 149 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 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 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 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 5 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 28 optimal weight: 0.0000 chunk 166 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 132 optimal weight: 0.1980 chunk 37 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.090293 restraints weight = 22323.574| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.32 r_work: 0.2942 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15250 Z= 0.110 Angle : 0.580 6.876 20720 Z= 0.277 Chirality : 0.044 0.226 2305 Planarity : 0.004 0.041 2625 Dihedral : 10.898 172.576 2170 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.90 % Allowed : 13.33 % Favored : 84.76 % 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: 1.08 (0.20), residues: 1830 helix: 1.27 (0.19), residues: 730 sheet: -0.36 (0.28), residues: 315 loop : 0.90 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 95 TYR 0.013 0.001 TYR E 53 PHE 0.011 0.001 PHE A 31 TRP 0.008 0.001 TRP D 79 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15240) covalent geometry : angle 0.58058 / 0.28 (20690) hydrogen bonds : bond 0.03079 / 2.10 ( 735) hydrogen bonds : angle 4.61512 / 3.21 ( 1815) link_TRANS : bond 0.00119 / 0.08 ( 10) link_TRANS : angle 0.38456 / 0.23 ( 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 258 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 227 MET cc_start: 0.8174 (mmm) cc_final: 0.7845 (tpp) REVERT: A 270 GLU cc_start: 0.5440 (mm-30) cc_final: 0.5161 (mm-30) REVERT: A 355 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5764 (mmm) REVERT: B 44 MET cc_start: 0.7865 (mtt) cc_final: 0.7560 (mtt) REVERT: B 47 MET cc_start: 0.7223 (mtt) cc_final: 0.5758 (mtt) REVERT: B 118 LYS cc_start: 0.8950 (tppt) cc_final: 0.8533 (tttt) REVERT: B 238 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8141 (mmmm) REVERT: B 249 THR cc_start: 0.9189 (m) cc_final: 0.8914 (p) REVERT: B 271 SER cc_start: 0.8598 (m) cc_final: 0.8355 (p) REVERT: B 284 LYS cc_start: 0.8243 (mttt) cc_final: 0.8025 (tttm) REVERT: B 285 CYS cc_start: 0.8763 (m) cc_final: 0.8478 (m) REVERT: B 314 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: C 44 MET cc_start: 0.8124 (mtt) cc_final: 0.7579 (mtt) REVERT: C 47 MET cc_start: 0.6563 (mtp) cc_final: 0.6023 (mtp) REVERT: C 118 LYS cc_start: 0.8785 (tppt) cc_final: 0.8289 (mtpt) REVERT: C 190 MET cc_start: 0.9047 (ttp) cc_final: 0.8789 (mtm) REVERT: C 276 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: D 44 MET cc_start: 0.3086 (ttt) cc_final: 0.2349 (ttt) REVERT: D 121 GLN cc_start: 0.8217 (tt0) cc_final: 0.7996 (tp40) REVERT: D 191 LYS cc_start: 0.8255 (tttt) cc_final: 0.7742 (ttmm) REVERT: D 205 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: D 206 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7445 (ttm170) REVERT: D 227 MET cc_start: 0.8264 (mmm) cc_final: 0.8000 (mmm) REVERT: D 316 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7853 (mm-30) REVERT: D 354 GLN cc_start: 0.8713 (pt0) cc_final: 0.8507 (pt0) REVERT: E 59 GLN cc_start: 0.8663 (tt0) cc_final: 0.8361 (mm-40) REVERT: E 92 ASN cc_start: 0.8019 (m-40) cc_final: 0.7358 (t0) REVERT: E 139 VAL cc_start: 0.9001 (t) cc_final: 0.8779 (m) REVERT: E 143 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8376 (t80) REVERT: E 237 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: E 314 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: E 333 PRO cc_start: 0.7945 (Cg_exo) cc_final: 0.7705 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8573 (pt0) cc_final: 0.8163 (pp30) outliers start: 30 outliers final: 18 residues processed: 246 average time/residue: 0.1102 time to fit residues: 40.9339 Evaluate side-chains 224 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 143 TYR Chi-restraints excluded: chain A residue 355 MET 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 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 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 205 GLU Chi-restraints excluded: chain D residue 278 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** 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 296 ASN ** 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 = 0.3229 r_free = 0.3229 target = 0.107650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.090134 restraints weight = 22188.461| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.33 r_work: 0.2887 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15250 Z= 0.115 Angle : 0.577 7.014 20720 Z= 0.274 Chirality : 0.044 0.226 2305 Planarity : 0.004 0.038 2625 Dihedral : 10.401 179.427 2170 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.03 % Allowed : 13.71 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.21 (0.20), residues: 1830 helix: 1.39 (0.19), residues: 730 sheet: -0.27 (0.29), residues: 315 loop : 0.94 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.010 0.001 TYR E 53 PHE 0.011 0.001 PHE A 31 TRP 0.008 0.001 TRP C 79 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (15240) covalent geometry : angle 0.57683 / 0.27 (20690) hydrogen bonds : bond 0.03042 / 2.08 ( 735) hydrogen bonds : angle 4.54886 / 3.16 ( 1815) link_TRANS : bond 0.00131 / 0.09 ( 10) link_TRANS : angle 0.36483 / 0.22 ( 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 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 176 MET cc_start: 0.8739 (mtp) cc_final: 0.8399 (mtt) REVERT: A 191 LYS cc_start: 0.8859 (tttt) cc_final: 0.8656 (tttm) REVERT: A 227 MET cc_start: 0.8182 (mmm) cc_final: 0.7863 (tpp) REVERT: A 270 GLU cc_start: 0.5517 (mm-30) cc_final: 0.5184 (mm-30) REVERT: A 355 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5771 (mmm) REVERT: B 47 MET cc_start: 0.7188 (mtt) cc_final: 0.6765 (mtm) REVERT: B 118 LYS cc_start: 0.8952 (tppt) cc_final: 0.8512 (tttt) REVERT: B 222 ASP cc_start: 0.8850 (t0) cc_final: 0.8582 (t70) REVERT: B 238 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8131 (mmmm) REVERT: B 271 SER cc_start: 0.8623 (m) cc_final: 0.8394 (p) REVERT: B 285 CYS cc_start: 0.8698 (m) cc_final: 0.8454 (m) REVERT: B 314 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: C 44 MET cc_start: 0.8034 (mtt) cc_final: 0.7631 (mtt) REVERT: C 47 MET cc_start: 0.6458 (mtp) cc_final: 0.6215 (mtp) REVERT: C 95 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7540 (mtm180) REVERT: C 118 LYS cc_start: 0.8779 (tppt) cc_final: 0.8291 (mtpt) REVERT: C 276 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: C 325 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: D 44 MET cc_start: 0.3181 (ttt) cc_final: 0.2247 (ttt) REVERT: D 191 LYS cc_start: 0.8346 (tttt) cc_final: 0.7850 (ttmm) REVERT: D 205 GLU cc_start: 0.8495 (mp0) cc_final: 0.8010 (mp0) REVERT: D 206 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7437 (ttm170) REVERT: D 316 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7892 (mm-30) REVERT: E 59 GLN cc_start: 0.8688 (tt0) cc_final: 0.8382 (mm-40) REVERT: E 139 VAL cc_start: 0.9002 (t) cc_final: 0.8784 (m) REVERT: E 143 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8372 (t80) REVERT: E 237 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7752 (mm-30) REVERT: E 314 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: E 333 PRO cc_start: 0.7944 (Cg_exo) cc_final: 0.7706 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8601 (pt0) cc_final: 0.8188 (pp30) REVERT: E 375 PHE cc_start: 0.5068 (OUTLIER) cc_final: 0.4467 (m-80) outliers start: 32 outliers final: 19 residues processed: 231 average time/residue: 0.1104 time to fit residues: 38.2620 Evaluate side-chains 226 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 143 TYR Chi-restraints excluded: chain A residue 355 MET 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 B residue 354 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 325 MET 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 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 47 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 154 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 0.0370 chunk 46 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087868 restraints weight = 22313.120| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.29 r_work: 0.2873 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15250 Z= 0.213 Angle : 0.644 7.066 20720 Z= 0.310 Chirality : 0.047 0.243 2305 Planarity : 0.005 0.039 2625 Dihedral : 10.111 176.322 2170 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.22 % Allowed : 13.78 % Favored : 84.00 % 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: 1.02 (0.20), residues: 1830 helix: 1.20 (0.19), residues: 730 sheet: -0.38 (0.29), residues: 320 loop : 0.87 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.013 0.001 TYR D 143 PHE 0.018 0.002 PHE D 375 TRP 0.012 0.002 TRP C 79 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (15240) covalent geometry : angle 0.64368 / 0.31 (20690) hydrogen bonds : bond 0.03706 / 2.50 ( 735) hydrogen bonds : angle 4.65152 / 3.23 ( 1815) link_TRANS : bond 0.00264 / 0.17 ( 10) link_TRANS : angle 0.54211 / 0.33 ( 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 235 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.419 Fit side-chains REVERT: A 44 MET cc_start: 0.7232 (mtt) cc_final: 0.6815 (mmm) REVERT: A 83 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 227 MET cc_start: 0.8168 (mmm) cc_final: 0.7856 (tpp) REVERT: A 270 GLU cc_start: 0.5382 (mm-30) cc_final: 0.4985 (mm-30) REVERT: A 355 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6053 (mmm) REVERT: B 44 MET cc_start: 0.7749 (mtt) cc_final: 0.7304 (mtt) REVERT: B 47 MET cc_start: 0.7149 (mtt) cc_final: 0.5759 (mtt) REVERT: B 118 LYS cc_start: 0.8986 (tppt) cc_final: 0.8559 (tttt) REVERT: B 162 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8633 (m-40) REVERT: B 238 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8131 (mmmm) REVERT: B 246 GLN cc_start: 0.8555 (mt0) cc_final: 0.8040 (mt0) REVERT: B 271 SER cc_start: 0.8690 (m) cc_final: 0.8478 (p) REVERT: B 285 CYS cc_start: 0.8781 (m) cc_final: 0.8363 (m) REVERT: B 286 ASP cc_start: 0.8068 (m-30) cc_final: 0.7406 (t70) REVERT: B 296 ASN cc_start: 0.8660 (m-40) cc_final: 0.8340 (m-40) REVERT: B 314 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: C 44 MET cc_start: 0.8019 (mtt) cc_final: 0.7618 (mtt) REVERT: C 47 MET cc_start: 0.6504 (mtp) cc_final: 0.6191 (mtp) REVERT: C 82 MET cc_start: 0.8368 (tpt) cc_final: 0.7699 (tpt) REVERT: C 95 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7607 (mtm180) REVERT: C 117 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7490 (tm-30) REVERT: C 118 LYS cc_start: 0.8761 (tppt) cc_final: 0.8437 (tptm) REVERT: C 276 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: C 289 ILE cc_start: 0.8280 (mt) cc_final: 0.8031 (tt) REVERT: C 333 PRO cc_start: 0.8321 (Cg_exo) cc_final: 0.8119 (Cg_endo) REVERT: D 44 MET cc_start: 0.3188 (ttt) cc_final: 0.1972 (ttt) REVERT: D 191 LYS cc_start: 0.8299 (tttt) cc_final: 0.7698 (ttmt) REVERT: D 205 GLU cc_start: 0.8687 (mp0) cc_final: 0.8260 (mp0) REVERT: D 206 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7540 (ttm170) REVERT: D 316 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7859 (mm-30) REVERT: E 59 GLN cc_start: 0.8714 (tt0) cc_final: 0.8422 (mm-40) REVERT: E 125 GLU cc_start: 0.8132 (tp30) cc_final: 0.7926 (tp30) REVERT: E 139 VAL cc_start: 0.9046 (t) cc_final: 0.8813 (m) REVERT: E 143 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8390 (t80) REVERT: E 237 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: E 314 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: E 333 PRO cc_start: 0.8026 (Cg_exo) cc_final: 0.7797 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8686 (pt0) cc_final: 0.8227 (pp30) REVERT: E 372 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.7058 (mtm110) REVERT: E 375 PHE cc_start: 0.4703 (OUTLIER) cc_final: 0.4285 (m-80) outliers start: 35 outliers final: 23 residues processed: 222 average time/residue: 0.1104 time to fit residues: 37.0472 Evaluate side-chains 223 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 355 MET 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 190 MET 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 72 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 178 LEU 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 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 346 LEU 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: 1.9990 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 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: 0.7980 chunk 113 optimal weight: 0.0970 chunk 119 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS ** B 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089637 restraints weight = 22541.034| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.27 r_work: 0.2918 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 15250 Z= 0.116 Angle : 0.586 6.888 20720 Z= 0.278 Chirality : 0.044 0.225 2305 Planarity : 0.004 0.041 2625 Dihedral : 9.452 156.536 2170 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.03 % Allowed : 14.22 % Favored : 83.75 % 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: 1.21 (0.20), residues: 1830 helix: 1.41 (0.19), residues: 730 sheet: -0.26 (0.29), residues: 315 loop : 0.91 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.008 0.001 TYR E 53 PHE 0.013 0.001 PHE D 375 TRP 0.008 0.001 TRP E 340 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15240) covalent geometry : angle 0.58635 / 0.28 (20690) hydrogen bonds : bond 0.03095 / 2.11 ( 735) hydrogen bonds : angle 4.51035 / 3.13 ( 1815) link_TRANS : bond 0.00133 / 0.09 ( 10) link_TRANS : angle 0.37076 / 0.22 ( 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 226 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.612 Fit side-chains REVERT: A 44 MET cc_start: 0.7213 (mtt) cc_final: 0.6759 (mmm) REVERT: A 83 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 176 MET cc_start: 0.8765 (mtp) cc_final: 0.8414 (mtt) REVERT: A 227 MET cc_start: 0.8162 (mmm) cc_final: 0.7437 (tpp) REVERT: A 269 MET cc_start: 0.8570 (mtt) cc_final: 0.8233 (mtp) REVERT: A 270 GLU cc_start: 0.5394 (mm-30) cc_final: 0.4549 (mm-30) REVERT: A 355 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5921 (mmm) REVERT: B 44 MET cc_start: 0.7714 (mtt) cc_final: 0.7361 (mtt) REVERT: B 47 MET cc_start: 0.7285 (mtt) cc_final: 0.5872 (mtt) REVERT: B 118 LYS cc_start: 0.8971 (tppt) cc_final: 0.8534 (tttt) REVERT: B 132 MET cc_start: 0.7783 (ptt) cc_final: 0.7575 (ptm) REVERT: B 238 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8151 (mmmm) REVERT: B 296 ASN cc_start: 0.8653 (m-40) cc_final: 0.8361 (m-40) REVERT: B 314 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: C 44 MET cc_start: 0.7905 (mtt) cc_final: 0.7390 (mtt) REVERT: C 47 MET cc_start: 0.6455 (mtp) cc_final: 0.6041 (mtp) REVERT: C 72 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: C 82 MET cc_start: 0.8385 (tpt) cc_final: 0.7626 (tpt) REVERT: C 95 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.7615 (mtm180) REVERT: C 118 LYS cc_start: 0.8752 (tppt) cc_final: 0.8482 (tptm) REVERT: C 276 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: D 191 LYS cc_start: 0.8305 (tttt) cc_final: 0.7685 (ttmt) REVERT: D 205 GLU cc_start: 0.8520 (mp0) cc_final: 0.8060 (mp0) REVERT: D 206 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7454 (ttm170) REVERT: D 316 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 125 GLU cc_start: 0.8123 (tp30) cc_final: 0.7896 (tp30) REVERT: E 139 VAL cc_start: 0.9042 (t) cc_final: 0.8836 (m) REVERT: E 143 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8411 (t80) REVERT: E 237 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7722 (mm-30) REVERT: E 314 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: E 325 MET cc_start: 0.8228 (mmp) cc_final: 0.8019 (mmm) REVERT: E 333 PRO cc_start: 0.8074 (Cg_exo) cc_final: 0.7849 (Cg_endo) REVERT: E 375 PHE cc_start: 0.4155 (OUTLIER) cc_final: 0.3658 (m-80) outliers start: 32 outliers final: 20 residues processed: 214 average time/residue: 0.1145 time to fit residues: 36.6634 Evaluate side-chains 215 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 355 MET 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 B residue 351 THR Chi-restraints excluded: chain C residue 72 GLU 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 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 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 375 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.088109 restraints weight = 22628.883| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.28 r_work: 0.2887 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15250 Z= 0.179 Angle : 0.624 9.126 20720 Z= 0.298 Chirality : 0.046 0.235 2305 Planarity : 0.004 0.037 2625 Dihedral : 9.167 136.027 2170 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.03 % Allowed : 14.41 % Favored : 83.56 % 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: 1.15 (0.20), residues: 1830 helix: 1.35 (0.19), residues: 730 sheet: -0.29 (0.29), residues: 315 loop : 0.89 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 95 TYR 0.014 0.001 TYR E 53 PHE 0.014 0.001 PHE C 124 TRP 0.010 0.002 TRP C 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (15240) covalent geometry : angle 0.62399 / 0.30 (20690) hydrogen bonds : bond 0.03422 / 2.32 ( 735) hydrogen bonds : angle 4.54646 / 3.16 ( 1815) link_TRANS : bond 0.00223 / 0.14 ( 10) link_TRANS : angle 0.46384 / 0.28 ( 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 221 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.679 Fit side-chains REVERT: A 44 MET cc_start: 0.7247 (mtt) cc_final: 0.6937 (mmm) REVERT: A 83 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 176 MET cc_start: 0.8805 (mtp) cc_final: 0.8451 (mtt) REVERT: A 227 MET cc_start: 0.8189 (mmm) cc_final: 0.7921 (tpp) REVERT: A 269 MET cc_start: 0.8609 (mtt) cc_final: 0.8283 (mtp) REVERT: A 270 GLU cc_start: 0.5522 (mm-30) cc_final: 0.4828 (mm-30) REVERT: A 355 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5816 (mmm) REVERT: B 118 LYS cc_start: 0.8978 (tppt) cc_final: 0.8532 (tttt) REVERT: B 132 MET cc_start: 0.8000 (ptt) cc_final: 0.7787 (ptm) REVERT: B 238 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8141 (mmmm) REVERT: B 283 MET cc_start: 0.7975 (mmm) cc_final: 0.7608 (mmt) REVERT: B 296 ASN cc_start: 0.8619 (m-40) cc_final: 0.8308 (m-40) REVERT: B 314 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: C 44 MET cc_start: 0.7930 (mtt) cc_final: 0.7447 (mtt) REVERT: C 47 MET cc_start: 0.6431 (mtp) cc_final: 0.6124 (mtp) REVERT: C 72 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: C 82 MET cc_start: 0.8397 (tpt) cc_final: 0.7687 (tpt) REVERT: C 95 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.7631 (mtm180) REVERT: C 117 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7467 (tm-30) REVERT: C 118 LYS cc_start: 0.8786 (tppt) cc_final: 0.8440 (tptm) REVERT: C 276 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: C 289 ILE cc_start: 0.8322 (mt) cc_final: 0.8079 (tt) REVERT: D 191 LYS cc_start: 0.8323 (tttt) cc_final: 0.7761 (ttmm) REVERT: D 205 GLU cc_start: 0.8663 (mp0) cc_final: 0.8244 (mp0) REVERT: D 206 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7514 (ttm170) REVERT: D 316 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7838 (mm-30) REVERT: E 79 TRP cc_start: 0.8547 (m100) cc_final: 0.8343 (m100) REVERT: E 125 GLU cc_start: 0.8143 (tp30) cc_final: 0.7914 (tp30) REVERT: E 132 MET cc_start: 0.8648 (ttt) cc_final: 0.8189 (ttt) REVERT: E 139 VAL cc_start: 0.9063 (t) cc_final: 0.8851 (m) REVERT: E 143 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8391 (t80) REVERT: E 237 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: E 314 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: E 333 PRO cc_start: 0.8126 (Cg_exo) cc_final: 0.7906 (Cg_endo) REVERT: E 375 PHE cc_start: 0.4232 (OUTLIER) cc_final: 0.3595 (m-80) outliers start: 32 outliers final: 21 residues processed: 211 average time/residue: 0.1128 time to fit residues: 35.8431 Evaluate side-chains 214 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 355 MET 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 B residue 351 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 178 LEU 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 149 THR Chi-restraints excluded: chain D residue 178 LEU 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 47 MET Chi-restraints excluded: chain E residue 129 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: 3.9990 chunk 129 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 48 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089721 restraints weight = 22281.962| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.26 r_work: 0.2901 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15250 Z= 0.127 Angle : 0.597 9.183 20720 Z= 0.283 Chirality : 0.044 0.227 2305 Planarity : 0.004 0.040 2625 Dihedral : 8.783 123.411 2170 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.97 % Allowed : 14.48 % Favored : 83.56 % 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: 1.23 (0.20), residues: 1830 helix: 1.45 (0.19), residues: 730 sheet: -0.25 (0.29), residues: 315 loop : 0.91 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 95 TYR 0.012 0.001 TYR E 53 PHE 0.013 0.001 PHE C 124 TRP 0.008 0.001 TRP G 1 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15240) covalent geometry : angle 0.59729 / 0.28 (20690) hydrogen bonds : bond 0.03089 / 2.11 ( 735) hydrogen bonds : angle 4.47572 / 3.11 ( 1815) link_TRANS : bond 0.00142 / 0.09 ( 10) link_TRANS : angle 0.38212 / 0.23 ( 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 221 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7289 (mtt) cc_final: 0.6875 (mmm) REVERT: A 83 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 176 MET cc_start: 0.8768 (mtp) cc_final: 0.8408 (mtt) REVERT: A 227 MET cc_start: 0.8177 (mmm) cc_final: 0.7461 (tpp) REVERT: A 269 MET cc_start: 0.8553 (mtt) cc_final: 0.8211 (mtp) REVERT: A 270 GLU cc_start: 0.5671 (mm-30) cc_final: 0.4822 (mm-30) REVERT: A 355 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5803 (mmm) REVERT: B 118 LYS cc_start: 0.8966 (tppt) cc_final: 0.8516 (tttt) REVERT: B 238 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8102 (mmmm) REVERT: B 283 MET cc_start: 0.8011 (mmm) cc_final: 0.7632 (mmt) REVERT: B 286 ASP cc_start: 0.8143 (m-30) cc_final: 0.7668 (t70) REVERT: B 296 ASN cc_start: 0.8646 (m-40) cc_final: 0.8342 (m-40) REVERT: B 314 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: B 360 GLN cc_start: 0.8233 (pt0) cc_final: 0.7918 (pt0) REVERT: C 44 MET cc_start: 0.7902 (mtt) cc_final: 0.7637 (mtt) REVERT: C 72 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: C 82 MET cc_start: 0.8397 (tpt) cc_final: 0.7633 (tpt) REVERT: C 95 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.7585 (mtt90) REVERT: C 118 LYS cc_start: 0.8766 (tppt) cc_final: 0.8491 (tptm) REVERT: C 276 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: C 355 MET cc_start: 0.8824 (mmm) cc_final: 0.8309 (mtp) REVERT: D 44 MET cc_start: 0.3118 (ttt) cc_final: 0.2840 (ttt) REVERT: D 191 LYS cc_start: 0.8338 (tttt) cc_final: 0.7775 (ttmm) REVERT: D 205 GLU cc_start: 0.8519 (mp0) cc_final: 0.8072 (mp0) REVERT: D 206 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7460 (ttm170) REVERT: D 227 MET cc_start: 0.8454 (mmm) cc_final: 0.8204 (mmm) REVERT: D 316 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 361 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7429 (mt-10) REVERT: E 79 TRP cc_start: 0.8484 (m100) cc_final: 0.8254 (m100) REVERT: E 125 GLU cc_start: 0.8096 (tp30) cc_final: 0.7869 (tp30) REVERT: E 139 VAL cc_start: 0.9052 (t) cc_final: 0.8851 (m) REVERT: E 143 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8402 (t80) REVERT: E 237 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: E 314 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: E 333 PRO cc_start: 0.8129 (Cg_exo) cc_final: 0.7906 (Cg_endo) REVERT: E 375 PHE cc_start: 0.3813 (OUTLIER) cc_final: 0.3486 (m-80) outliers start: 31 outliers final: 20 residues processed: 211 average time/residue: 0.1161 time to fit residues: 36.8941 Evaluate side-chains 212 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 355 MET 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 B residue 351 THR Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 178 LEU 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 106 THR 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 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 129 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 138 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 1 optimal weight: 0.0270 chunk 108 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 181 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 354 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.092860 restraints weight = 22227.962| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.24 r_work: 0.2939 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15250 Z= 0.096 Angle : 0.570 8.115 20720 Z= 0.268 Chirality : 0.043 0.220 2305 Planarity : 0.004 0.039 2625 Dihedral : 8.386 123.071 2170 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.59 % Allowed : 14.73 % Favored : 83.68 % 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: 1.40 (0.20), residues: 1830 helix: 1.64 (0.19), residues: 730 sheet: -0.15 (0.29), residues: 315 loop : 0.93 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 95 TYR 0.011 0.001 TYR E 53 PHE 0.014 0.001 PHE C 124 TRP 0.013 0.001 TRP D 86 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (15240) covalent geometry : angle 0.57015 / 0.27 (20690) hydrogen bonds : bond 0.02829 / 1.96 ( 735) hydrogen bonds : angle 4.39419 / 3.06 ( 1815) link_TRANS : bond 0.00071 / 0.05 ( 10) link_TRANS : angle 0.28360 / 0.18 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.06 seconds wall clock time: 56 minutes 15.49 seconds (3375.49 seconds total)