Starting phenix.real_space_refine on Sun Mar 17 01:29:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1l_27134/03_2024/8d1l_27134_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1l_27134/03_2024/8d1l_27134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1l_27134/03_2024/8d1l_27134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1l_27134/03_2024/8d1l_27134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1l_27134/03_2024/8d1l_27134_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1l_27134/03_2024/8d1l_27134_updated.pdb" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 P 5 5.49 5 S 80 5.16 5 Cl 1 4.86 5 C 10905 2.51 5 N 2550 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C ASP 335": "OD1" <-> "OD2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 303": "OD1" <-> "OD2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 303": "OD1" <-> "OD2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E ASP 335": "OD1" <-> "OD2" Residue "E GLU 371": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E GLU 374": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16306 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {' CA': 1, ' CL': 1, 'MC3': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 8.75, per 1000 atoms: 0.54 Number of scatterers: 16306 At special positions: 0 Unit cell: (109.56, 107.07, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 80 16.00 P 5 15.00 O 2760 8.00 N 2550 7.00 C 10905 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 2.8 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 0 sheets defined 62.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 16 through 22 removed outlier: 4.004A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 21 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 22' Processing helix chain 'B' and resid 28 through 52 removed outlier: 5.616A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 72 Processing helix chain 'B' and resid 76 through 98 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 119 through 143 Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 204 through 229 Processing helix chain 'B' and resid 234 through 254 removed outlier: 3.979A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 275 through 294 removed outlier: 3.751A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 323 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 16 through 22 removed outlier: 4.004A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 21 " --> pdb=" O PHE C 17 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 22' Processing helix chain 'C' and resid 28 through 52 removed outlier: 5.616A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 72 Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 119 through 143 Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 183 through 197 Processing helix chain 'C' and resid 204 through 229 Processing helix chain 'C' and resid 234 through 254 removed outlier: 3.979A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 275 through 294 removed outlier: 3.751A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 323 Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 16 through 22 removed outlier: 4.004A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 16 through 22' Processing helix chain 'A' and resid 28 through 52 removed outlier: 5.616A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 72 Processing helix chain 'A' and resid 76 through 98 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 119 through 143 Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 204 through 229 Processing helix chain 'A' and resid 234 through 254 removed outlier: 3.979A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 275 through 294 removed outlier: 3.751A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 16 through 22 removed outlier: 4.004A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 16 through 22' Processing helix chain 'D' and resid 28 through 52 removed outlier: 5.616A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 72 Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 104 through 113 Processing helix chain 'D' and resid 119 through 143 Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 204 through 229 Processing helix chain 'D' and resid 234 through 254 removed outlier: 3.978A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 275 through 294 removed outlier: 3.751A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 323 Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'E' and resid 7 through 9 No H-bonds generated for 'chain 'E' and resid 7 through 9' Processing helix chain 'E' and resid 16 through 22 removed outlier: 4.004A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU E 22 " --> pdb=" O SER E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 16 through 22' Processing helix chain 'E' and resid 28 through 52 removed outlier: 5.616A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 72 Processing helix chain 'E' and resid 76 through 98 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 119 through 143 Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 165 through 173 Processing helix chain 'E' and resid 183 through 197 Processing helix chain 'E' and resid 204 through 229 Processing helix chain 'E' and resid 234 through 254 removed outlier: 3.979A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 275 through 294 removed outlier: 3.750A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' 820 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2420 1.31 - 1.43: 4840 1.43 - 1.56: 9330 1.56 - 1.68: 10 1.68 - 1.81: 135 Bond restraints: 16735 Sorted by residual: bond pdb=" C11 MC3 A 604 " pdb=" O3 MC3 A 604 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C11 MC3 B 603 " pdb=" O3 MC3 B 603 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C11 MC3 C 603 " pdb=" O3 MC3 C 603 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C11 MC3 E 604 " pdb=" O3 MC3 E 604 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C11 MC3 D 603 " pdb=" O3 MC3 D 603 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 16730 not shown) Histogram of bond angle deviations from ideal: 91.40 - 99.93: 15 99.93 - 108.46: 813 108.46 - 116.99: 10556 116.99 - 125.52: 10806 125.52 - 134.05: 370 Bond angle restraints: 22560 Sorted by residual: angle pdb=" C41 MC3 E 606 " pdb=" C42 MC3 E 606 " pdb=" C43 MC3 E 606 " ideal model delta sigma weight residual 113.45 91.40 22.05 3.00e+00 1.11e-01 5.40e+01 angle pdb=" C41 MC3 A 606 " pdb=" C42 MC3 A 606 " pdb=" C43 MC3 A 606 " ideal model delta sigma weight residual 113.45 91.40 22.05 3.00e+00 1.11e-01 5.40e+01 angle pdb=" C41 MC3 B 605 " pdb=" C42 MC3 B 605 " pdb=" C43 MC3 B 605 " ideal model delta sigma weight residual 113.45 91.42 22.03 3.00e+00 1.11e-01 5.39e+01 angle pdb=" C41 MC3 D 605 " pdb=" C42 MC3 D 605 " pdb=" C43 MC3 D 605 " ideal model delta sigma weight residual 113.45 91.42 22.03 3.00e+00 1.11e-01 5.39e+01 angle pdb=" C41 MC3 C 605 " pdb=" C42 MC3 C 605 " pdb=" C43 MC3 C 605 " ideal model delta sigma weight residual 113.45 91.43 22.02 3.00e+00 1.11e-01 5.39e+01 ... (remaining 22555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 9220 26.43 - 52.87: 575 52.87 - 79.30: 120 79.30 - 105.74: 15 105.74 - 132.17: 5 Dihedral angle restraints: 9935 sinusoidal: 4370 harmonic: 5565 Sorted by residual: dihedral pdb=" C33 MC3 A 604 " pdb=" C31 MC3 A 604 " pdb=" C32 MC3 A 604 " pdb=" O2 MC3 A 604 " ideal model delta sinusoidal sigma weight residual 175.52 43.35 132.17 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C33 MC3 E 604 " pdb=" C31 MC3 E 604 " pdb=" C32 MC3 E 604 " pdb=" O2 MC3 E 604 " ideal model delta sinusoidal sigma weight residual 175.52 43.35 132.17 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C33 MC3 D 603 " pdb=" C31 MC3 D 603 " pdb=" C32 MC3 D 603 " pdb=" O2 MC3 D 603 " ideal model delta sinusoidal sigma weight residual 175.52 43.35 132.17 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 9932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1612 0.034 - 0.067: 566 0.067 - 0.101: 120 0.101 - 0.134: 73 0.134 - 0.168: 14 Chirality restraints: 2385 Sorted by residual: chirality pdb=" CA LEU D 138 " pdb=" N LEU D 138 " pdb=" C LEU D 138 " pdb=" CB LEU D 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA LEU B 138 " pdb=" N LEU B 138 " pdb=" C LEU B 138 " pdb=" CB LEU B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA LEU A 138 " pdb=" N LEU A 138 " pdb=" C LEU A 138 " pdb=" CB LEU A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 2382 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 276 " -0.007 2.00e-02 2.50e+03 1.13e-02 2.24e+00 pdb=" CG PHE A 276 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 276 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 276 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 276 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 276 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 276 " 0.007 2.00e-02 2.50e+03 1.12e-02 2.20e+00 pdb=" CG PHE D 276 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE D 276 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 276 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 276 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 276 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 276 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 276 " -0.007 2.00e-02 2.50e+03 1.12e-02 2.19e+00 pdb=" CG PHE E 276 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE E 276 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE E 276 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 276 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 276 " -0.000 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2790 2.76 - 3.29: 15846 3.29 - 3.83: 29592 3.83 - 4.36: 36493 4.36 - 4.90: 59220 Nonbonded interactions: 143941 Sorted by model distance: nonbonded pdb=" NH2 ARG E 51 " pdb=" OD2 ASP E 270 " model vdw 2.222 2.520 nonbonded pdb=" NH2 ARG A 51 " pdb=" OD2 ASP A 270 " model vdw 2.222 2.520 nonbonded pdb=" NH2 ARG C 51 " pdb=" OD2 ASP C 270 " model vdw 2.222 2.520 nonbonded pdb=" NH2 ARG B 51 " pdb=" OD2 ASP B 270 " model vdw 2.222 2.520 nonbonded pdb=" NH2 ARG D 51 " pdb=" OD2 ASP D 270 " model vdw 2.223 2.520 ... (remaining 143936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 377 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42)) or (resid 605 through 606 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C40 or name C41 or name C42 or name C43 or name C44)) or (resid 607 t \ hrough 608 and (name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C42)) or resid 609)) selection = (chain 'B' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'C' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'D' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'E' and (resid 2 through 377 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42)) or (resid 605 through 606 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C40 or name C41 or name C42 or name C43 or name C44)) or (resid 607 t \ hrough 608 and (name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C42)) or resid 609)) } 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.440 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 44.430 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 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 : 0.005 0.071 16735 Z= 0.308 Angle : 0.943 22.051 22560 Z= 0.406 Chirality : 0.040 0.168 2385 Planarity : 0.004 0.024 2770 Dihedral : 17.688 132.174 6345 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.18 % Allowed : 9.14 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 1870 helix: 1.54 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : 0.59 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 309 HIS 0.005 0.002 HIS E 178 PHE 0.025 0.002 PHE A 276 TYR 0.022 0.001 TYR C 97 ARG 0.003 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 1.777 Fit side-chains REVERT: C 193 MET cc_start: 0.9014 (tpt) cc_final: 0.8762 (tpp) REVERT: A 68 TYR cc_start: 0.6613 (t80) cc_final: 0.6399 (t80) REVERT: A 193 MET cc_start: 0.8984 (tpt) cc_final: 0.8757 (tpp) REVERT: A 370 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8368 (tttm) REVERT: D 276 PHE cc_start: 0.7633 (t80) cc_final: 0.7334 (m-80) REVERT: D 370 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8148 (ttpp) REVERT: E 276 PHE cc_start: 0.7694 (t80) cc_final: 0.7459 (m-80) REVERT: E 370 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8400 (ttpp) outliers start: 20 outliers final: 7 residues processed: 231 average time/residue: 1.3907 time to fit residues: 353.0911 Evaluate side-chains 190 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain E residue 178 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16735 Z= 0.168 Angle : 0.478 7.683 22560 Z= 0.245 Chirality : 0.037 0.150 2385 Planarity : 0.004 0.027 2770 Dihedral : 13.610 127.225 2654 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.18 % Allowed : 10.80 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 1870 helix: 1.84 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.53 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 185 HIS 0.004 0.001 HIS D 326 PHE 0.017 0.001 PHE E 276 TYR 0.018 0.001 TYR E 97 ARG 0.005 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 2.061 Fit side-chains REVERT: B 119 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: C 119 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: C 193 MET cc_start: 0.8999 (tpt) cc_final: 0.8765 (tpp) REVERT: C 276 PHE cc_start: 0.7962 (m-80) cc_final: 0.7199 (t80) REVERT: A 68 TYR cc_start: 0.6290 (t80) cc_final: 0.5877 (t80) REVERT: A 276 PHE cc_start: 0.7886 (m-10) cc_final: 0.7384 (t80) REVERT: A 370 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8456 (tttm) REVERT: A 372 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8105 (mt-10) REVERT: D 119 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7006 (tp30) REVERT: D 370 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8456 (ttpp) REVERT: D 372 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8081 (mt-10) REVERT: E 61 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7163 (tpp) REVERT: E 119 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: E 276 PHE cc_start: 0.7685 (t80) cc_final: 0.7447 (m-80) REVERT: E 370 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8388 (ttpp) outliers start: 20 outliers final: 12 residues processed: 213 average time/residue: 1.4130 time to fit residues: 331.8189 Evaluate side-chains 211 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 139 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16735 Z= 0.179 Angle : 0.472 7.201 22560 Z= 0.244 Chirality : 0.038 0.150 2385 Planarity : 0.004 0.028 2770 Dihedral : 12.725 121.964 2648 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.89 % Allowed : 10.68 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.19), residues: 1870 helix: 1.89 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : 0.53 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 309 HIS 0.004 0.001 HIS D 326 PHE 0.016 0.001 PHE C 248 TYR 0.019 0.001 TYR D 97 ARG 0.005 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.955 Fit side-chains REVERT: B 119 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: C 61 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6585 (tmt) REVERT: C 119 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: C 193 MET cc_start: 0.9003 (tpt) cc_final: 0.8776 (tpp) REVERT: A 276 PHE cc_start: 0.7828 (m-10) cc_final: 0.7370 (t80) REVERT: A 370 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8483 (tttm) REVERT: D 119 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7002 (tp30) REVERT: D 370 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8489 (ttpp) REVERT: E 119 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: E 276 PHE cc_start: 0.7737 (t80) cc_final: 0.7492 (m-80) outliers start: 32 outliers final: 11 residues processed: 220 average time/residue: 1.3586 time to fit residues: 330.9470 Evaluate side-chains 212 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B 376 GLN C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN A 178 HIS ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16735 Z= 0.368 Angle : 0.576 7.978 22560 Z= 0.299 Chirality : 0.044 0.157 2385 Planarity : 0.004 0.032 2770 Dihedral : 12.693 122.862 2646 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.01 % Allowed : 10.62 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.19), residues: 1870 helix: 1.57 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : 0.25 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 309 HIS 0.006 0.002 HIS B 178 PHE 0.028 0.002 PHE C 248 TYR 0.027 0.002 TYR D 97 ARG 0.005 0.001 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 1.717 Fit side-chains REVERT: B 119 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: C 61 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6609 (tmt) REVERT: C 119 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: C 193 MET cc_start: 0.8996 (tpt) cc_final: 0.8762 (tpp) REVERT: C 276 PHE cc_start: 0.8042 (m-80) cc_final: 0.7225 (t80) REVERT: A 51 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.5812 (mpt-90) REVERT: A 68 TYR cc_start: 0.6502 (t80) cc_final: 0.6148 (t80) REVERT: A 276 PHE cc_start: 0.7884 (m-10) cc_final: 0.7328 (t80) REVERT: A 370 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8456 (tttm) REVERT: D 119 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7021 (tp30) REVERT: D 355 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7661 (ttt180) REVERT: D 370 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8551 (ttpp) REVERT: E 119 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: E 276 PHE cc_start: 0.7753 (t80) cc_final: 0.7483 (m-80) outliers start: 34 outliers final: 13 residues processed: 217 average time/residue: 1.3523 time to fit residues: 323.0866 Evaluate side-chains 219 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16735 Z= 0.307 Angle : 0.546 7.507 22560 Z= 0.283 Chirality : 0.042 0.155 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.449 121.824 2644 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.71 % Allowed : 11.15 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.19), residues: 1870 helix: 1.66 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.39 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 309 HIS 0.005 0.001 HIS D 178 PHE 0.025 0.002 PHE B 248 TYR 0.025 0.002 TYR D 97 ARG 0.006 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.813 Fit side-chains REVERT: B 119 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: C 61 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6605 (tmt) REVERT: C 119 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: C 193 MET cc_start: 0.9003 (tpt) cc_final: 0.8802 (tpp) REVERT: C 276 PHE cc_start: 0.7985 (m-80) cc_final: 0.7200 (t80) REVERT: A 51 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.5786 (mpt-90) REVERT: A 68 TYR cc_start: 0.6470 (t80) cc_final: 0.6116 (t80) REVERT: A 276 PHE cc_start: 0.7848 (m-10) cc_final: 0.7316 (t80) REVERT: A 370 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8457 (tttm) REVERT: D 119 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: D 355 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7650 (ttt180) REVERT: D 370 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8565 (ttpp) REVERT: E 119 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: E 276 PHE cc_start: 0.7706 (t80) cc_final: 0.7492 (m-80) outliers start: 29 outliers final: 12 residues processed: 211 average time/residue: 1.4213 time to fit residues: 329.9845 Evaluate side-chains 214 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16735 Z= 0.205 Angle : 0.503 7.208 22560 Z= 0.257 Chirality : 0.039 0.150 2385 Planarity : 0.004 0.033 2770 Dihedral : 11.977 120.057 2644 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.71 % Allowed : 11.62 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 1870 helix: 1.72 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : 0.36 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 309 HIS 0.004 0.001 HIS D 326 PHE 0.018 0.001 PHE C 248 TYR 0.021 0.002 TYR D 97 ARG 0.006 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 1.789 Fit side-chains REVERT: B 119 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 262 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8177 (mmmt) REVERT: C 61 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6679 (tmt) REVERT: C 119 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: C 276 PHE cc_start: 0.7889 (m-80) cc_final: 0.7200 (t80) REVERT: A 51 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.5793 (mpt-90) REVERT: A 68 TYR cc_start: 0.6233 (t80) cc_final: 0.5845 (t80) REVERT: A 276 PHE cc_start: 0.7785 (m-10) cc_final: 0.7306 (t80) REVERT: A 370 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8443 (tttm) REVERT: D 119 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: D 355 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7689 (ttt180) REVERT: D 370 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8552 (ttpp) REVERT: E 119 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: E 276 PHE cc_start: 0.7651 (t80) cc_final: 0.7445 (m-80) outliers start: 29 outliers final: 13 residues processed: 219 average time/residue: 1.4501 time to fit residues: 348.3334 Evaluate side-chains 221 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 178 optimal weight: 0.0980 chunk 111 optimal weight: 0.0470 chunk 108 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16735 Z= 0.136 Angle : 0.462 6.652 22560 Z= 0.232 Chirality : 0.036 0.148 2385 Planarity : 0.004 0.031 2770 Dihedral : 11.312 117.115 2642 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.30 % Allowed : 12.27 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1870 helix: 1.82 (0.14), residues: 1175 sheet: None (None), residues: 0 loop : 0.37 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 93 HIS 0.002 0.001 HIS C 178 PHE 0.018 0.001 PHE E 80 TYR 0.015 0.001 TYR D 97 ARG 0.006 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 1.935 Fit side-chains REVERT: B 119 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: C 119 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: C 276 PHE cc_start: 0.7823 (m-80) cc_final: 0.7217 (t80) REVERT: A 276 PHE cc_start: 0.7754 (m-10) cc_final: 0.7323 (t80) REVERT: A 370 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8403 (tttm) REVERT: D 119 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: D 355 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7681 (ttt180) REVERT: D 370 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8550 (ttpp) REVERT: E 119 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7532 (mp0) outliers start: 22 outliers final: 8 residues processed: 222 average time/residue: 1.5429 time to fit residues: 375.2162 Evaluate side-chains 213 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 0.2980 chunk 162 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16735 Z= 0.156 Angle : 0.481 8.198 22560 Z= 0.240 Chirality : 0.037 0.148 2385 Planarity : 0.004 0.031 2770 Dihedral : 11.011 116.263 2640 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.06 % Allowed : 12.68 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.19), residues: 1870 helix: 1.85 (0.14), residues: 1175 sheet: None (None), residues: 0 loop : 0.37 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 309 HIS 0.003 0.001 HIS D 178 PHE 0.013 0.001 PHE C 276 TYR 0.018 0.001 TYR D 97 ARG 0.004 0.000 ARG E 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 1.835 Fit side-chains REVERT: B 119 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: C 119 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: A 276 PHE cc_start: 0.7744 (m-10) cc_final: 0.7321 (t80) REVERT: A 370 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8395 (tttm) REVERT: D 119 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: D 355 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7686 (ttt180) REVERT: D 370 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8568 (ttpp) REVERT: E 119 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: E 276 PHE cc_start: 0.7613 (t80) cc_final: 0.7277 (m-80) outliers start: 18 outliers final: 9 residues processed: 214 average time/residue: 1.4979 time to fit residues: 351.3857 Evaluate side-chains 210 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16735 Z= 0.246 Angle : 0.534 9.462 22560 Z= 0.270 Chirality : 0.040 0.220 2385 Planarity : 0.004 0.032 2770 Dihedral : 11.207 119.126 2640 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.24 % Allowed : 12.74 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 1870 helix: 1.80 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : 0.38 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 309 HIS 0.005 0.001 HIS D 326 PHE 0.021 0.001 PHE C 248 TYR 0.024 0.002 TYR D 97 ARG 0.006 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.916 Fit side-chains REVERT: B 119 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: C 119 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: C 276 PHE cc_start: 0.7783 (m-80) cc_final: 0.7113 (t80) REVERT: A 51 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.5950 (mpt-90) REVERT: A 276 PHE cc_start: 0.7802 (m-10) cc_final: 0.7325 (t80) REVERT: A 370 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8422 (tttm) REVERT: D 119 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: D 355 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7650 (ttt180) REVERT: D 370 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8556 (ttpp) REVERT: E 119 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7518 (mp0) outliers start: 21 outliers final: 9 residues processed: 214 average time/residue: 1.4765 time to fit residues: 346.9503 Evaluate side-chains 208 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16735 Z= 0.179 Angle : 0.510 11.308 22560 Z= 0.253 Chirality : 0.039 0.279 2385 Planarity : 0.004 0.031 2770 Dihedral : 10.836 118.406 2640 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.94 % Allowed : 13.22 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1870 helix: 1.83 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : 0.38 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 309 HIS 0.004 0.001 HIS D 326 PHE 0.016 0.001 PHE C 248 TYR 0.020 0.001 TYR D 97 ARG 0.005 0.000 ARG E 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 1.880 Fit side-chains REVERT: B 119 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: C 119 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 51 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.5915 (mpt-90) REVERT: A 262 LYS cc_start: 0.8276 (mttt) cc_final: 0.7950 (mttt) REVERT: A 276 PHE cc_start: 0.7771 (m-10) cc_final: 0.7353 (t80) REVERT: A 370 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8402 (tttm) REVERT: D 119 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7014 (tp30) REVERT: D 355 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7695 (ttt180) REVERT: D 370 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8553 (ttpp) REVERT: E 119 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7519 (mp0) outliers start: 16 outliers final: 11 residues processed: 206 average time/residue: 1.5344 time to fit residues: 345.6439 Evaluate side-chains 212 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.080352 restraints weight = 20224.889| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.64 r_work: 0.2861 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16735 Z= 0.175 Angle : 0.506 11.384 22560 Z= 0.251 Chirality : 0.039 0.288 2385 Planarity : 0.004 0.031 2770 Dihedral : 10.514 117.028 2640 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.00 % Allowed : 13.16 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 1870 helix: 1.74 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.35 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 309 HIS 0.003 0.001 HIS D 326 PHE 0.015 0.001 PHE C 248 TYR 0.019 0.001 TYR B 97 ARG 0.005 0.000 ARG E 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6014.17 seconds wall clock time: 107 minutes 17.80 seconds (6437.80 seconds total)