Starting phenix.real_space_refine on Tue Nov 18 15:39:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t1y_10363/11_2025/6t1y_10363.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t1y_10363/11_2025/6t1y_10363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t1y_10363/11_2025/6t1y_10363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t1y_10363/11_2025/6t1y_10363.map" model { file = "/net/cci-nas-00/data/ceres_data/6t1y_10363/11_2025/6t1y_10363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t1y_10363/11_2025/6t1y_10363.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9410 2.51 5 N 2510 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/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: 3.71, 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: 1.43 Conformation dependent library (CDL) restraints added in 645.3 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: 0.70 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: 2.83 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3772 1.32 - 1.44: 3417 1.44 - 1.56: 7856 1.56 - 1.68: 5 1.68 - 1.81: 190 Bond restraints: 15240 Sorted by residual: bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" CA EEP G 2 " pdb=" C EEP G 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" CA EEP F 2 " pdb=" C EEP F 2 " ideal model delta sigma weight residual 1.572 1.472 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18109 2.18 - 4.36: 2188 4.36 - 6.54: 243 6.54 - 8.72: 109 8.72 - 10.90: 41 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C ALA A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta sigma weight residual 119.66 128.66 -9.00 7.30e-01 1.88e+00 1.52e+02 angle pdb=" C ALA E 331 " pdb=" N PRO E 332 " pdb=" CA PRO E 332 " ideal model delta sigma weight residual 119.66 128.64 -8.98 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA C 331 " pdb=" N PRO C 332 " pdb=" CA PRO C 332 " ideal model delta sigma weight residual 119.66 128.64 -8.98 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA D 331 " pdb=" N PRO D 332 " pdb=" CA PRO D 332 " ideal model delta sigma weight residual 119.66 128.63 -8.97 7.30e-01 1.88e+00 1.51e+02 angle pdb=" C ALA B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta sigma weight residual 119.66 128.56 -8.90 7.30e-01 1.88e+00 1.49e+02 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.95: 9034 29.95 - 59.90: 96 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: 855 0.043 - 0.087: 764 0.087 - 0.130: 390 0.130 - 0.174: 223 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- 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 0.100 15250 Z= 1.099 Angle : 1.607 10.897 20720 Z= 1.083 Chirality : 0.082 0.217 2305 Planarity : 0.006 0.060 2625 Dihedral : 12.482 149.759 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 covalent geometry : bond 0.01742 (15240) covalent geometry : angle 1.60146 (20690) hydrogen bonds : bond 0.17274 ( 735) hydrogen bonds : angle 8.15669 ( 1815) link_TRANS : bond 0.00376 ( 10) link_TRANS : angle 3.71206 ( 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 : 0.605 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: 0.1415 time to fit residues: 93.7281 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 : 0.543 ------------------------------------------------------------------------------- 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 173 HIS D 354 GLN E 173 HIS ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097461 restraints weight = 22342.803| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.12 r_work: 0.3004 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15250 Z= 0.153 Angle : 0.695 8.674 20720 Z= 0.346 Chirality : 0.048 0.211 2305 Planarity : 0.005 0.043 2625 Dihedral : 12.699 163.204 2175 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.51 (0.20), residues: 1830 helix: 0.64 (0.19), residues: 730 sheet: -0.66 (0.28), residues: 320 loop : 0.77 (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 0.019 0.002 PHE D 352 TRP 0.018 0.002 TRP F 1 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00326 (15240) covalent geometry : angle 0.69434 (20690) hydrogen bonds : bond 0.04067 ( 735) hydrogen bonds : angle 5.37406 ( 1815) link_TRANS : bond 0.00130 ( 10) link_TRANS : angle 0.97362 ( 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 314 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8791 (mtp) cc_final: 0.8428 (mtt) REVERT: A 194 THR cc_start: 0.8957 (m) cc_final: 0.8386 (p) REVERT: A 227 MET cc_start: 0.8232 (mmm) cc_final: 0.7990 (tpp) REVERT: A 259 GLU cc_start: 0.8708 (tp30) cc_final: 0.8466 (tp30) REVERT: A 314 GLN cc_start: 0.8704 (tp40) cc_final: 0.8359 (tt0) REVERT: B 47 MET cc_start: 0.7567 (mtt) cc_final: 0.6518 (mtm) REVERT: B 118 LYS cc_start: 0.8831 (tppt) cc_final: 0.8527 (tttt) REVERT: B 211 ASP cc_start: 0.8796 (t70) cc_final: 0.8013 (m-30) REVERT: B 238 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8257 (mmmm) REVERT: B 271 SER cc_start: 0.8552 (m) cc_final: 0.8216 (p) REVERT: B 284 LYS cc_start: 0.8098 (mttt) cc_final: 0.7821 (mtpt) REVERT: B 285 CYS cc_start: 0.8438 (m) cc_final: 0.8169 (m) REVERT: C 44 MET cc_start: 0.7991 (mtt) cc_final: 0.7791 (mtt) REVERT: C 119 MET cc_start: 0.8197 (ttp) cc_final: 0.7930 (ttp) REVERT: C 187 ASP cc_start: 0.8813 (t70) cc_final: 0.8578 (t0) REVERT: C 276 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: C 286 ASP cc_start: 0.7846 (t0) cc_final: 0.7615 (m-30) REVERT: C 289 ILE cc_start: 0.8336 (mt) cc_final: 0.8101 (tt) REVERT: C 314 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8074 (tm-30) REVERT: D 123 MET cc_start: 0.8003 (mmt) cc_final: 0.7645 (mmt) REVERT: D 191 LYS cc_start: 0.8107 (tttt) cc_final: 0.7815 (ttmm) REVERT: D 206 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7738 (ttm170) REVERT: D 316 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7869 (mm-30) REVERT: D 353 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7822 (mm110) REVERT: E 40 HIS cc_start: 0.8387 (m-70) cc_final: 0.8001 (m-70) REVERT: E 44 MET cc_start: 0.1825 (tpt) cc_final: 0.1371 (mtp) REVERT: E 53 TYR cc_start: 0.8786 (m-80) cc_final: 0.8498 (m-80) REVERT: E 59 GLN cc_start: 0.8521 (tt0) cc_final: 0.8224 (mm-40) REVERT: E 191 LYS cc_start: 0.8852 (tttt) cc_final: 0.8556 (ttmt) REVERT: E 333 PRO cc_start: 0.7642 (Cg_exo) cc_final: 0.7395 (Cg_endo) outliers start: 31 outliers final: 16 residues processed: 304 average time/residue: 0.1250 time to fit residues: 56.2688 Evaluate side-chains 237 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 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 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: 1.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.086210 restraints weight = 22720.847| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.30 r_work: 0.2808 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15250 Z= 0.313 Angle : 0.761 7.256 20720 Z= 0.380 Chirality : 0.051 0.256 2305 Planarity : 0.006 0.053 2625 Dihedral : 12.053 174.109 2170 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.16 % Allowed : 10.67 % 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: 0.50 (0.19), residues: 1830 helix: 0.66 (0.19), residues: 730 sheet: -0.64 (0.28), residues: 315 loop : 0.70 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 290 TYR 0.017 0.002 TYR D 143 PHE 0.020 0.003 PHE B 375 TRP 0.016 0.003 TRP D 340 HIS 0.007 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00747 (15240) covalent geometry : angle 0.76036 (20690) hydrogen bonds : bond 0.04775 ( 735) hydrogen bonds : angle 5.14319 ( 1815) link_TRANS : bond 0.00495 ( 10) link_TRANS : angle 0.86993 ( 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 260 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9019 (t) cc_final: 0.8800 (m) REVERT: A 83 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 194 THR cc_start: 0.9120 (m) cc_final: 0.8695 (p) REVERT: A 227 MET cc_start: 0.8205 (mmm) cc_final: 0.7856 (tpp) REVERT: A 270 GLU cc_start: 0.5468 (mm-30) cc_final: 0.5091 (mm-30) REVERT: A 355 MET cc_start: 0.6060 (mtt) cc_final: 0.5647 (mmt) REVERT: B 41 GLN cc_start: 0.9052 (tt0) cc_final: 0.8821 (tt0) REVERT: B 59 GLN cc_start: 0.8294 (tt0) cc_final: 0.8090 (tp40) REVERT: B 118 LYS cc_start: 0.8942 (tppt) cc_final: 0.8571 (tttt) REVERT: B 211 ASP cc_start: 0.8732 (t70) cc_final: 0.7902 (m-30) REVERT: B 238 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8162 (mmmm) REVERT: B 271 SER cc_start: 0.8631 (m) cc_final: 0.8368 (p) REVERT: B 285 CYS cc_start: 0.8754 (m) cc_final: 0.8463 (m) REVERT: B 296 ASN cc_start: 0.8648 (m-40) cc_final: 0.8266 (m110) REVERT: C 82 MET cc_start: 0.8438 (tpt) cc_final: 0.7716 (tpt) REVERT: C 83 GLU cc_start: 0.8701 (tt0) cc_final: 0.8404 (mt-10) REVERT: C 117 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7563 (tm-30) REVERT: C 119 MET cc_start: 0.8215 (ttp) cc_final: 0.7964 (ttp) REVERT: C 190 MET cc_start: 0.9049 (ttp) cc_final: 0.8787 (mtm) REVERT: C 276 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: C 286 ASP cc_start: 0.7965 (t0) cc_final: 0.7621 (m-30) REVERT: C 289 ILE cc_start: 0.8356 (mt) cc_final: 0.8089 (tt) REVERT: C 353 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8001 (mm-40) REVERT: D 205 GLU cc_start: 0.8668 (mp0) cc_final: 0.8242 (mp0) REVERT: D 206 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7598 (ttm170) REVERT: D 316 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7895 (mm-30) REVERT: E 40 HIS cc_start: 0.8542 (m-70) cc_final: 0.8089 (m-70) REVERT: E 44 MET cc_start: 0.2089 (tpt) cc_final: 0.1795 (ttt) REVERT: E 59 GLN cc_start: 0.8655 (tt0) cc_final: 0.8361 (mm-40) REVERT: E 107 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8283 (tp30) REVERT: E 125 GLU cc_start: 0.8088 (tp30) cc_final: 0.7769 (tp30) REVERT: E 143 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8328 (t80) REVERT: E 333 PRO cc_start: 0.8118 (Cg_exo) cc_final: 0.7859 (Cg_endo) outliers start: 34 outliers final: 24 residues processed: 249 average time/residue: 0.1230 time to fit residues: 46.0761 Evaluate side-chains 219 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 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: 0.6980 chunk 41 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 149 optimal weight: 0.0030 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 0.0770 chunk 151 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.092177 restraints weight = 21970.005| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.30 r_work: 0.2892 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15250 Z= 0.105 Angle : 0.596 6.758 20720 Z= 0.285 Chirality : 0.044 0.226 2305 Planarity : 0.004 0.041 2625 Dihedral : 11.242 173.219 2170 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.78 % Allowed : 12.25 % Favored : 85.97 % 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: 0.94 (0.20), residues: 1830 helix: 1.12 (0.19), residues: 730 sheet: -0.51 (0.28), residues: 315 loop : 0.89 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 95 TYR 0.008 0.001 TYR D 69 PHE 0.016 0.001 PHE B 375 TRP 0.009 0.001 TRP E 340 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00217 (15240) covalent geometry : angle 0.59585 (20690) hydrogen bonds : bond 0.03106 ( 735) hydrogen bonds : angle 4.70064 ( 1815) link_TRANS : bond 0.00112 ( 10) link_TRANS : angle 0.45623 ( 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 261 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.477 Fit side-chains REVERT: A 83 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7786 (tm-30) REVERT: A 100 GLU cc_start: 0.8281 (tp30) cc_final: 0.8016 (tp30) REVERT: A 194 THR cc_start: 0.9144 (m) cc_final: 0.8603 (p) REVERT: A 227 MET cc_start: 0.8189 (mmm) cc_final: 0.7863 (tpp) REVERT: A 270 GLU cc_start: 0.5428 (mm-30) cc_final: 0.5020 (mm-30) REVERT: B 47 MET cc_start: 0.7377 (mtt) cc_final: 0.6606 (mtm) REVERT: B 118 LYS cc_start: 0.8939 (tppt) cc_final: 0.8528 (tttt) REVERT: B 211 ASP cc_start: 0.8731 (t70) cc_final: 0.7927 (m-30) REVERT: B 222 ASP cc_start: 0.8840 (t0) cc_final: 0.8551 (t0) REVERT: B 238 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8151 (mmmm) REVERT: B 271 SER cc_start: 0.8612 (m) cc_final: 0.8360 (p) REVERT: B 285 CYS cc_start: 0.8715 (m) cc_final: 0.8468 (m) REVERT: B 296 ASN cc_start: 0.8624 (m-40) cc_final: 0.8197 (m110) REVERT: B 314 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: C 118 LYS cc_start: 0.8785 (tppt) cc_final: 0.8267 (mtpt) REVERT: C 190 MET cc_start: 0.8999 (ttp) cc_final: 0.8789 (mtm) REVERT: C 276 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: D 205 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: D 206 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7422 (ttm170) REVERT: D 227 MET cc_start: 0.8266 (mmm) cc_final: 0.7952 (mmm) REVERT: D 316 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7921 (mm-30) REVERT: E 40 HIS cc_start: 0.8490 (m-70) cc_final: 0.8148 (m-70) REVERT: E 59 GLN cc_start: 0.8650 (tt0) cc_final: 0.8363 (mm-40) REVERT: E 125 GLU cc_start: 0.8011 (tp30) cc_final: 0.7758 (tp30) REVERT: E 139 VAL cc_start: 0.8960 (t) cc_final: 0.8725 (m) REVERT: E 143 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8343 (t80) REVERT: E 237 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7743 (mm-30) REVERT: E 333 PRO cc_start: 0.7959 (Cg_exo) cc_final: 0.7718 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8589 (pt0) cc_final: 0.8202 (pp30) outliers start: 28 outliers final: 14 residues processed: 247 average time/residue: 0.1132 time to fit residues: 42.5394 Evaluate side-chains 221 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 276 GLU 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 E residue 43 VAL Chi-restraints excluded: chain E residue 126 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 0.0970 chunk 132 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 chunk 178 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 D 353 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.090476 restraints weight = 22294.912| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.32 r_work: 0.2905 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15250 Z= 0.123 Angle : 0.589 6.988 20720 Z= 0.280 Chirality : 0.045 0.228 2305 Planarity : 0.004 0.039 2625 Dihedral : 10.741 170.733 2170 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.97 % Allowed : 12.76 % Favored : 85.27 % 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: 1.11 (0.20), residues: 1830 helix: 1.27 (0.19), residues: 730 sheet: -0.32 (0.28), residues: 315 loop : 0.92 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 95 TYR 0.008 0.001 TYR E 362 PHE 0.020 0.001 PHE C 124 TRP 0.008 0.001 TRP C 79 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00282 (15240) covalent geometry : angle 0.58887 (20690) hydrogen bonds : bond 0.03147 ( 735) hydrogen bonds : angle 4.59426 ( 1815) link_TRANS : bond 0.00186 ( 10) link_TRANS : angle 0.44891 ( 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 244 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7766 (tm-30) REVERT: A 194 THR cc_start: 0.9134 (m) cc_final: 0.8624 (p) REVERT: A 227 MET cc_start: 0.8281 (mmm) cc_final: 0.7929 (tpp) REVERT: A 270 GLU cc_start: 0.5436 (mm-30) cc_final: 0.5182 (mm-30) REVERT: B 44 MET cc_start: 0.7888 (mtt) cc_final: 0.7657 (mtt) REVERT: B 47 MET cc_start: 0.7572 (mtt) cc_final: 0.6489 (mtm) REVERT: B 118 LYS cc_start: 0.8946 (tppt) cc_final: 0.8539 (tttt) REVERT: B 222 ASP cc_start: 0.8866 (t0) cc_final: 0.8620 (t70) REVERT: B 238 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8138 (mmmm) REVERT: B 249 THR cc_start: 0.9191 (m) cc_final: 0.8919 (p) REVERT: B 271 SER cc_start: 0.8621 (m) cc_final: 0.8418 (p) REVERT: B 285 CYS cc_start: 0.8694 (m) cc_final: 0.8354 (m) REVERT: B 296 ASN cc_start: 0.8682 (m-40) cc_final: 0.8273 (m110) REVERT: B 314 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: C 44 MET cc_start: 0.8217 (mtt) cc_final: 0.7678 (mtt) REVERT: C 118 LYS cc_start: 0.8777 (tppt) cc_final: 0.8275 (mtpt) REVERT: C 190 MET cc_start: 0.8997 (ttp) cc_final: 0.8795 (mtm) REVERT: C 276 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: D 191 LYS cc_start: 0.8281 (tttt) cc_final: 0.7765 (ttmm) REVERT: D 205 GLU cc_start: 0.8489 (mp0) cc_final: 0.7988 (mp0) REVERT: D 206 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7473 (ttm170) REVERT: D 316 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7879 (mm-30) REVERT: D 355 MET cc_start: 0.8430 (mtp) cc_final: 0.8168 (mtp) REVERT: E 59 GLN cc_start: 0.8668 (tt0) cc_final: 0.8380 (mm-40) REVERT: E 92 ASN cc_start: 0.8007 (m-40) cc_final: 0.7350 (t0) REVERT: E 125 GLU cc_start: 0.8018 (tp30) cc_final: 0.7760 (tp30) REVERT: E 139 VAL cc_start: 0.9007 (t) cc_final: 0.8782 (m) REVERT: E 143 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8351 (t80) REVERT: E 237 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: E 314 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: E 333 PRO cc_start: 0.7957 (Cg_exo) cc_final: 0.7714 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8566 (pt0) cc_final: 0.8153 (pp30) outliers start: 31 outliers final: 22 residues processed: 230 average time/residue: 0.1205 time to fit residues: 42.1055 Evaluate side-chains 220 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 205 GLU 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: 0.9980 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093723 restraints weight = 21787.070| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.21 r_work: 0.2891 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15250 Z= 0.177 Angle : 0.612 7.096 20720 Z= 0.293 Chirality : 0.046 0.236 2305 Planarity : 0.004 0.038 2625 Dihedral : 10.454 170.597 2170 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.54 % Allowed : 13.14 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1830 helix: 1.26 (0.19), residues: 730 sheet: -0.37 (0.29), residues: 320 loop : 0.88 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.010 0.001 TYR D 143 PHE 0.015 0.001 PHE C 124 TRP 0.009 0.001 TRP A 86 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00419 (15240) covalent geometry : angle 0.61221 (20690) hydrogen bonds : bond 0.03386 ( 735) hydrogen bonds : angle 4.60727 ( 1815) link_TRANS : bond 0.00277 ( 10) link_TRANS : angle 0.54170 ( 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 248 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7158 (mtt) cc_final: 0.6575 (mmm) REVERT: A 83 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 194 THR cc_start: 0.9194 (m) cc_final: 0.8691 (p) REVERT: A 227 MET cc_start: 0.8237 (mmm) cc_final: 0.7966 (tpp) REVERT: A 270 GLU cc_start: 0.5588 (mm-30) cc_final: 0.5232 (mm-30) REVERT: B 118 LYS cc_start: 0.8964 (tppt) cc_final: 0.8553 (tttt) REVERT: B 222 ASP cc_start: 0.8848 (t0) cc_final: 0.8592 (t70) REVERT: B 238 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8163 (mmmm) REVERT: B 244 ASP cc_start: 0.8557 (p0) cc_final: 0.8298 (p0) REVERT: B 285 CYS cc_start: 0.8754 (m) cc_final: 0.8317 (m) REVERT: B 314 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: C 95 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.7599 (mtm180) REVERT: C 118 LYS cc_start: 0.8859 (tppt) cc_final: 0.8361 (mtpt) REVERT: C 187 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: C 190 MET cc_start: 0.9037 (ttp) cc_final: 0.8806 (mtm) REVERT: C 276 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: C 325 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: D 44 MET cc_start: 0.3378 (ttt) cc_final: 0.2977 (ttt) REVERT: D 191 LYS cc_start: 0.8372 (tttt) cc_final: 0.7873 (ttmm) REVERT: D 205 GLU cc_start: 0.8588 (mp0) cc_final: 0.8155 (mp0) REVERT: D 206 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7547 (ttm170) REVERT: D 227 MET cc_start: 0.8354 (mmm) cc_final: 0.8062 (mmm) REVERT: D 316 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7880 (mm-30) REVERT: D 355 MET cc_start: 0.8454 (mtp) cc_final: 0.8230 (mtt) REVERT: E 59 GLN cc_start: 0.8705 (tt0) cc_final: 0.8454 (mm-40) REVERT: E 125 GLU cc_start: 0.7960 (tp30) cc_final: 0.7679 (tp30) REVERT: E 139 VAL cc_start: 0.9049 (t) cc_final: 0.8819 (m) REVERT: E 143 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8298 (t80) REVERT: E 237 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: E 283 MET cc_start: 0.8314 (mmm) cc_final: 0.8072 (mmm) REVERT: E 314 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: E 333 PRO cc_start: 0.8029 (Cg_exo) cc_final: 0.7795 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8592 (pt0) cc_final: 0.8182 (pp30) REVERT: E 375 PHE cc_start: 0.4404 (OUTLIER) cc_final: 0.3947 (m-80) outliers start: 40 outliers final: 25 residues processed: 231 average time/residue: 0.1237 time to fit residues: 43.0555 Evaluate side-chains 227 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 ASP 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 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 154 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 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 371 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 40 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.090497 restraints weight = 22048.382| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.30 r_work: 0.2916 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15250 Z= 0.136 Angle : 0.594 6.829 20720 Z= 0.282 Chirality : 0.045 0.230 2305 Planarity : 0.004 0.039 2625 Dihedral : 10.005 175.812 2170 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.10 % Allowed : 13.71 % Favored : 84.19 % 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: 1.20 (0.20), residues: 1830 helix: 1.37 (0.19), residues: 730 sheet: -0.22 (0.29), residues: 325 loop : 0.93 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.008 0.001 TYR E 362 PHE 0.012 0.001 PHE C 124 TRP 0.008 0.001 TRP E 340 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00318 (15240) covalent geometry : angle 0.59456 (20690) hydrogen bonds : bond 0.03163 ( 735) hydrogen bonds : angle 4.53102 ( 1815) link_TRANS : bond 0.00206 ( 10) link_TRANS : angle 0.47934 ( 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 237 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 227 MET cc_start: 0.8212 (mmm) cc_final: 0.7447 (tpp) REVERT: A 270 GLU cc_start: 0.5284 (mm-30) cc_final: 0.4996 (mm-30) REVERT: B 44 MET cc_start: 0.7745 (mtt) cc_final: 0.7411 (mtt) REVERT: B 118 LYS cc_start: 0.8975 (tppt) cc_final: 0.8537 (tttt) REVERT: B 222 ASP cc_start: 0.8851 (t0) cc_final: 0.8592 (t70) REVERT: B 238 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8126 (mmmm) REVERT: B 296 ASN cc_start: 0.8676 (m-40) cc_final: 0.8384 (m-40) REVERT: B 314 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: C 44 MET cc_start: 0.7998 (mtt) cc_final: 0.7575 (ttm) REVERT: C 47 MET cc_start: 0.5801 (mpp) cc_final: 0.5162 (mpp) REVERT: C 95 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7594 (mtm180) REVERT: C 118 LYS cc_start: 0.8792 (tppt) cc_final: 0.8530 (tptm) REVERT: C 187 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8502 (m-30) REVERT: C 190 MET cc_start: 0.9052 (ttp) cc_final: 0.8843 (mtm) REVERT: C 276 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: D 44 MET cc_start: 0.3289 (ttt) cc_final: 0.2946 (ttt) REVERT: D 191 LYS cc_start: 0.8292 (tttt) cc_final: 0.7686 (ttmt) REVERT: D 205 GLU cc_start: 0.8558 (mp0) cc_final: 0.8096 (mp0) REVERT: D 206 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7483 (ttm170) REVERT: D 227 MET cc_start: 0.8264 (mmm) cc_final: 0.7962 (mmm) REVERT: D 316 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7880 (mm-30) REVERT: E 59 GLN cc_start: 0.8698 (tt0) cc_final: 0.8395 (mm-40) REVERT: E 92 ASN cc_start: 0.8043 (m-40) cc_final: 0.7323 (t0) REVERT: E 125 GLU cc_start: 0.7955 (tp30) cc_final: 0.7665 (tp30) REVERT: E 132 MET cc_start: 0.8740 (ttt) cc_final: 0.8522 (ttt) REVERT: E 139 VAL cc_start: 0.9027 (t) cc_final: 0.8803 (m) REVERT: E 143 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.8358 (t80) REVERT: E 237 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: E 283 MET cc_start: 0.8345 (mmm) cc_final: 0.8051 (mmm) REVERT: E 314 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: E 333 PRO cc_start: 0.8058 (Cg_exo) cc_final: 0.7823 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8650 (pt0) cc_final: 0.8111 (pp30) REVERT: E 372 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.7009 (mtm110) REVERT: E 375 PHE cc_start: 0.3994 (OUTLIER) cc_final: 0.2689 (m-80) outliers start: 33 outliers final: 22 residues processed: 226 average time/residue: 0.1252 time to fit residues: 42.5733 Evaluate side-chains 215 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 375 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 131 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.089283 restraints weight = 22561.947| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.30 r_work: 0.2907 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15250 Z= 0.141 Angle : 0.602 7.040 20720 Z= 0.285 Chirality : 0.045 0.230 2305 Planarity : 0.004 0.037 2625 Dihedral : 9.779 177.108 2170 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.29 % Allowed : 14.16 % 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: 1.21 (0.20), residues: 1830 helix: 1.40 (0.19), residues: 730 sheet: -0.17 (0.30), residues: 315 loop : 0.87 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.008 0.001 TYR D 143 PHE 0.023 0.001 PHE D 375 TRP 0.009 0.001 TRP A 86 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00331 (15240) covalent geometry : angle 0.60239 (20690) hydrogen bonds : bond 0.03200 ( 735) hydrogen bonds : angle 4.51462 ( 1815) link_TRANS : bond 0.00207 ( 10) link_TRANS : angle 0.47094 ( 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 228 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7045 (mtt) cc_final: 0.6707 (mmm) REVERT: A 83 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 176 MET cc_start: 0.8787 (mtp) cc_final: 0.8432 (mtt) REVERT: A 227 MET cc_start: 0.8231 (mmm) cc_final: 0.7558 (tpp) REVERT: A 269 MET cc_start: 0.8570 (mtt) cc_final: 0.8235 (mtp) REVERT: A 270 GLU cc_start: 0.5364 (mm-30) cc_final: 0.4738 (mm-30) REVERT: A 355 MET cc_start: 0.6282 (mmt) cc_final: 0.6033 (mmt) REVERT: B 118 LYS cc_start: 0.8985 (tppt) cc_final: 0.8558 (tttt) REVERT: B 222 ASP cc_start: 0.8857 (t0) cc_final: 0.8594 (t70) REVERT: B 238 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8119 (mmmm) REVERT: B 283 MET cc_start: 0.8254 (mmm) cc_final: 0.7996 (mmt) REVERT: B 296 ASN cc_start: 0.8658 (m-40) cc_final: 0.8375 (m-40) REVERT: B 314 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: C 47 MET cc_start: 0.5709 (mpp) cc_final: 0.4903 (mpp) REVERT: C 95 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7595 (mtm180) REVERT: C 118 LYS cc_start: 0.8729 (tppt) cc_final: 0.8451 (tptm) REVERT: C 187 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: C 190 MET cc_start: 0.9035 (ttp) cc_final: 0.8825 (mtm) REVERT: C 276 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: D 44 MET cc_start: 0.3172 (ttt) cc_final: 0.2844 (ttt) REVERT: D 82 MET cc_start: 0.8346 (tpt) cc_final: 0.8117 (tpp) REVERT: D 191 LYS cc_start: 0.8305 (tttt) cc_final: 0.7740 (ttmm) REVERT: D 205 GLU cc_start: 0.8570 (mp0) cc_final: 0.8120 (mp0) REVERT: D 206 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7493 (ttm170) REVERT: D 316 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7887 (mm-30) REVERT: E 125 GLU cc_start: 0.7984 (tp30) cc_final: 0.7697 (tp30) REVERT: E 132 MET cc_start: 0.8686 (ttt) cc_final: 0.8466 (ttt) REVERT: E 139 VAL cc_start: 0.9041 (t) cc_final: 0.8813 (m) REVERT: E 143 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8366 (t80) REVERT: E 237 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: E 283 MET cc_start: 0.8442 (mmm) cc_final: 0.8139 (mmm) REVERT: E 314 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: E 333 PRO cc_start: 0.8030 (Cg_exo) cc_final: 0.7799 (Cg_endo) REVERT: E 354 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8333 (pp30) REVERT: E 372 ARG cc_start: 0.7369 (mtm-85) cc_final: 0.7165 (mtm110) REVERT: E 375 PHE cc_start: 0.3994 (OUTLIER) cc_final: 0.2935 (m-80) outliers start: 36 outliers final: 23 residues processed: 215 average time/residue: 0.1247 time to fit residues: 40.1949 Evaluate side-chains 219 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 354 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: 0.6980 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.089138 restraints weight = 22484.882| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.30 r_work: 0.2833 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15250 Z= 0.139 Angle : 0.609 9.046 20720 Z= 0.288 Chirality : 0.045 0.229 2305 Planarity : 0.004 0.038 2625 Dihedral : 9.547 165.777 2170 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.90 % Allowed : 14.60 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.20), residues: 1830 helix: 1.44 (0.19), residues: 730 sheet: -0.14 (0.30), residues: 315 loop : 0.92 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.008 0.001 TYR D 143 PHE 0.016 0.001 PHE D 375 TRP 0.009 0.001 TRP A 86 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00325 (15240) covalent geometry : angle 0.60920 (20690) hydrogen bonds : bond 0.03170 ( 735) hydrogen bonds : angle 4.50237 ( 1815) link_TRANS : bond 0.00198 ( 10) link_TRANS : angle 0.46398 ( 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 223 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7100 (mtt) cc_final: 0.6725 (mmm) REVERT: A 83 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 176 MET cc_start: 0.8767 (mtp) cc_final: 0.8412 (mtt) REVERT: A 227 MET cc_start: 0.8209 (mmm) cc_final: 0.7528 (tpp) REVERT: A 269 MET cc_start: 0.8544 (mtt) cc_final: 0.8226 (mtp) REVERT: A 270 GLU cc_start: 0.5456 (mm-30) cc_final: 0.4780 (mm-30) REVERT: A 316 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8345 (mm-30) REVERT: A 355 MET cc_start: 0.6335 (mmt) cc_final: 0.5935 (mmt) REVERT: B 118 LYS cc_start: 0.8982 (tppt) cc_final: 0.8567 (tttt) REVERT: B 238 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8114 (mmmm) REVERT: B 283 MET cc_start: 0.8189 (mmm) cc_final: 0.7918 (mmt) REVERT: B 296 ASN cc_start: 0.8682 (m-40) cc_final: 0.8393 (m-40) REVERT: B 314 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: B 360 GLN cc_start: 0.8303 (pt0) cc_final: 0.7995 (pt0) REVERT: C 44 MET cc_start: 0.7375 (mtt) cc_final: 0.7070 (ttm) REVERT: C 95 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7623 (mtm180) REVERT: C 118 LYS cc_start: 0.8722 (tppt) cc_final: 0.8438 (tptm) REVERT: C 187 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: C 190 MET cc_start: 0.9028 (ttp) cc_final: 0.8827 (mtm) REVERT: C 276 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: D 44 MET cc_start: 0.3176 (ttt) cc_final: 0.2787 (ttt) REVERT: D 191 LYS cc_start: 0.8343 (tttt) cc_final: 0.7779 (ttmm) REVERT: D 205 GLU cc_start: 0.8572 (mp0) cc_final: 0.8107 (mp0) REVERT: D 206 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7440 (ttm170) REVERT: D 316 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7887 (mm-30) REVERT: D 375 PHE cc_start: 0.5442 (t80) cc_final: 0.5000 (t80) REVERT: E 125 GLU cc_start: 0.7978 (tp30) cc_final: 0.7689 (tp30) REVERT: E 132 MET cc_start: 0.8670 (ttt) cc_final: 0.8435 (ttt) REVERT: E 139 VAL cc_start: 0.9037 (t) cc_final: 0.8824 (m) REVERT: E 143 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8390 (t80) REVERT: E 237 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: E 283 MET cc_start: 0.8439 (mmm) cc_final: 0.8126 (mmm) REVERT: E 314 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: E 333 PRO cc_start: 0.8020 (Cg_exo) cc_final: 0.7791 (Cg_endo) REVERT: E 375 PHE cc_start: 0.3981 (OUTLIER) cc_final: 0.2248 (m-80) outliers start: 30 outliers final: 21 residues processed: 212 average time/residue: 0.1247 time to fit residues: 39.7011 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 : 0.574 ------------------------------------------------------------------------------- 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 B residue 43 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 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 205 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 346 LEU 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: 0.0470 chunk 129 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 121 optimal weight: 0.0050 chunk 168 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.092345 restraints weight = 22025.065| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.25 r_work: 0.2932 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15250 Z= 0.100 Angle : 0.584 10.538 20720 Z= 0.273 Chirality : 0.044 0.224 2305 Planarity : 0.004 0.040 2625 Dihedral : 8.891 132.997 2170 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.71 % Allowed : 14.86 % Favored : 83.43 % 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: 1.41 (0.20), residues: 1830 helix: 1.59 (0.19), residues: 730 sheet: -0.11 (0.29), residues: 315 loop : 0.97 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.008 0.001 TYR C 306 PHE 0.012 0.001 PHE C 124 TRP 0.009 0.001 TRP G 1 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00223 (15240) covalent geometry : angle 0.58405 (20690) hydrogen bonds : bond 0.02862 ( 735) hydrogen bonds : angle 4.43548 ( 1815) link_TRANS : bond 0.00125 ( 10) link_TRANS : angle 0.35350 ( 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 240 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7170 (mtt) cc_final: 0.6807 (mmm) REVERT: A 83 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7773 (tm-30) REVERT: A 227 MET cc_start: 0.8229 (mmm) cc_final: 0.7560 (tpp) REVERT: A 269 MET cc_start: 0.8573 (mtt) cc_final: 0.8221 (mtp) REVERT: A 270 GLU cc_start: 0.5539 (mm-30) cc_final: 0.5097 (mm-30) REVERT: A 355 MET cc_start: 0.6232 (mmt) cc_final: 0.5976 (mmt) REVERT: B 118 LYS cc_start: 0.8967 (tppt) cc_final: 0.8532 (tttt) REVERT: B 222 ASP cc_start: 0.8826 (t0) cc_final: 0.8556 (t70) REVERT: B 238 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8103 (mmmm) REVERT: B 283 MET cc_start: 0.8175 (mmm) cc_final: 0.7895 (mmt) REVERT: B 285 CYS cc_start: 0.8819 (m) cc_final: 0.8575 (m) REVERT: B 296 ASN cc_start: 0.8618 (m-40) cc_final: 0.8340 (m-40) REVERT: B 314 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: C 95 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.7542 (mtt90) REVERT: C 118 LYS cc_start: 0.8755 (tppt) cc_final: 0.8475 (tptm) REVERT: C 187 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: C 276 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: D 44 MET cc_start: 0.3022 (ttt) cc_final: 0.2713 (ttt) REVERT: D 191 LYS cc_start: 0.8342 (tttt) cc_final: 0.7781 (ttmm) REVERT: D 205 GLU cc_start: 0.8434 (mp0) cc_final: 0.7947 (mp0) REVERT: D 206 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7426 (ttm170) REVERT: D 316 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7841 (mm-30) REVERT: D 361 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7407 (mt-10) REVERT: E 132 MET cc_start: 0.8610 (ttt) cc_final: 0.8387 (ttt) REVERT: E 143 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8361 (t80) REVERT: E 237 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: E 283 MET cc_start: 0.8406 (mmm) cc_final: 0.8089 (mmm) REVERT: E 314 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7486 (tt0) outliers start: 27 outliers final: 19 residues processed: 231 average time/residue: 0.1278 time to fit residues: 44.2250 Evaluate side-chains 215 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 B residue 47 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 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 205 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 138 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.0050 chunk 1 optimal weight: 0.0470 chunk 108 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN B 59 GLN B 121 GLN B 162 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN ** E 12 ASN ** 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 = 0.3251 r_free = 0.3251 target = 0.109466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.092126 restraints weight = 22230.859| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.30 r_work: 0.2919 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15250 Z= 0.097 Angle : 0.587 9.416 20720 Z= 0.272 Chirality : 0.043 0.223 2305 Planarity : 0.004 0.038 2625 Dihedral : 8.576 122.870 2170 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.59 % Allowed : 15.11 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.20), residues: 1830 helix: 1.67 (0.19), residues: 730 sheet: -0.07 (0.30), residues: 315 loop : 0.99 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.011 0.001 TYR D 169 PHE 0.011 0.001 PHE E 31 TRP 0.011 0.001 TRP D 86 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00217 (15240) covalent geometry : angle 0.58714 (20690) hydrogen bonds : bond 0.02812 ( 735) hydrogen bonds : angle 4.37141 ( 1815) link_TRANS : bond 0.00103 ( 10) link_TRANS : angle 0.31318 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3519.17 seconds wall clock time: 61 minutes 17.55 seconds (3677.55 seconds total)