Starting phenix.real_space_refine on Thu Feb 22 04:31:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy9_22525/02_2024/7jy9_22525_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy9_22525/02_2024/7jy9_22525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy9_22525/02_2024/7jy9_22525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy9_22525/02_2024/7jy9_22525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy9_22525/02_2024/7jy9_22525_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jy9_22525/02_2024/7jy9_22525_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 49032 atoms to isotropic. 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 P 138 5.49 5 Mg 9 5.21 5 S 116 5.16 5 C 15182 2.51 5 N 4306 2.21 5 O 5098 1.98 5 H 24183 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A GLU 4": "OE1" <-> "OE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "D ASP 3": "OD1" <-> "OD2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 100": "OD1" <-> "OD2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E GLU 314": "OE1" <-> "OE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "F ASP 3": "OD1" <-> "OD2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 100": "OD1" <-> "OD2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G GLU 156": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 311": "OD1" <-> "OD2" Residue "G GLU 318": "OE1" <-> "OE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 233": "OE1" <-> "OE2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "H TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "I ASP 36": "OD1" <-> "OD2" Residue "I GLU 38": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 100": "OD1" <-> "OD2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I GLU 156": "OE1" <-> "OE2" Residue "I ASP 161": "OD1" <-> "OD2" Residue "I PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I ASP 276": "OD1" <-> "OD2" Residue "I GLU 325": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 49032 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "B" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "C" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "D" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "E" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "F" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "G" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "H" Number of atoms: 5085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5085 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "I" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4575 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain: "T" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1334 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "U" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1322 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "S" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 833 Classifications: {'DNA': 27} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.88, per 1000 atoms: 0.36 Number of scatterers: 49032 At special positions: 0 Unit cell: (130.424, 128.232, 201.664, 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) S 116 16.00 P 138 15.00 Mg 9 11.99 O 5098 8.00 N 4306 7.00 C 15182 6.00 H 24183 1.00 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: 29.76 Conformation dependent library (CDL) restraints added in 3.5 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5324 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 36 sheets defined 39.5% alpha, 19.0% beta 39 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 19.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 72 through 86 removed outlier: 3.604A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 166 through 185 removed outlier: 3.515A pdb=" N ARG A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLY A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.635A pdb=" N ASP A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'B' and resid 2 through 21 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 45 through 51 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.527A pdb=" N ARG B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 270 through 280 removed outlier: 3.530A pdb=" N ASP B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 327 removed outlier: 3.586A pdb=" N LYS B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 72 through 85 Processing helix chain 'C' and resid 101 through 107 Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 166 through 185 removed outlier: 4.947A pdb=" N GLY C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.554A pdb=" N ASP C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 313 through 327 Processing helix chain 'D' and resid 2 through 21 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 45 through 51 Processing helix chain 'D' and resid 72 through 85 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 152 through 156 Processing helix chain 'D' and resid 166 through 185 removed outlier: 3.564A pdb=" N ARG D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 313 through 327 Processing helix chain 'E' and resid 2 through 20 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.636A pdb=" N GLU E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 107 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 166 through 185 removed outlier: 3.543A pdb=" N ARG E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 218 Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'F' and resid 2 through 21 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 33 through 35 No H-bonds generated for 'chain 'F' and resid 33 through 35' Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.633A pdb=" N GLU F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 166 through 185 removed outlier: 4.692A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.607A pdb=" N ASP F 276 " --> pdb=" O GLY F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 313 through 327 Processing helix chain 'G' and resid 2 through 21 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 45 through 51 Processing helix chain 'G' and resid 72 through 85 Processing helix chain 'G' and resid 101 through 107 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 166 through 185 removed outlier: 4.653A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 218 Processing helix chain 'G' and resid 270 through 280 removed outlier: 3.675A pdb=" N ASP G 276 " --> pdb=" O GLY G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 313 through 327 Processing helix chain 'H' and resid 2 through 20 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 45 through 51 Processing helix chain 'H' and resid 72 through 85 Processing helix chain 'H' and resid 101 through 107 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 152 through 156 Processing helix chain 'H' and resid 166 through 185 removed outlier: 3.584A pdb=" N ARG H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 218 Processing helix chain 'H' and resid 270 through 280 removed outlier: 3.520A pdb=" N ASP H 276 " --> pdb=" O GLY H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 313 through 327 Processing helix chain 'I' and resid 45 through 50 Processing helix chain 'I' and resid 72 through 86 removed outlier: 3.673A pdb=" N GLU I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 106 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 152 through 156 Processing helix chain 'I' and resid 166 through 185 removed outlier: 3.511A pdb=" N ARG I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY I 180 " --> pdb=" O ARG I 176 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 218 Processing helix chain 'I' and resid 270 through 280 removed outlier: 3.575A pdb=" N ASP I 276 " --> pdb=" O GLY I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 311 Processing helix chain 'I' and resid 313 through 327 Processing sheet with id= A, first strand: chain 'A' and resid 257 through 263 removed outlier: 6.334A pdb=" N ARG A 222 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 221 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 189 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 64 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE A 191 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLY A 66 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN A 193 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 115 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP A 94 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A 117 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 195 through 197 Processing sheet with id= C, first strand: chain 'A' and resid 229 through 233 removed outlier: 6.740A pdb=" N GLU A 233 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.570A pdb=" N TYR A 293 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 257 through 263 removed outlier: 6.382A pdb=" N ARG B 222 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 221 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 189 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE B 64 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE B 191 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY B 66 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 193 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 115 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP B 94 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 117 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 195 through 197 Processing sheet with id= G, first strand: chain 'B' and resid 229 through 233 removed outlier: 6.582A pdb=" N GLU B 233 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 290 through 293 removed outlier: 6.493A pdb=" N TYR B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 257 through 263 removed outlier: 6.293A pdb=" N ARG C 222 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 221 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU C 189 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE C 64 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE C 191 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N GLY C 66 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN C 193 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU C 115 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER C 117 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 195 through 197 Processing sheet with id= K, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.589A pdb=" N TYR C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 229 through 233 removed outlier: 6.467A pdb=" N GLU C 233 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 257 through 263 removed outlier: 6.337A pdb=" N ARG D 222 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 221 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU D 189 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE D 64 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE D 191 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLY D 66 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN D 193 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU D 115 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 195 through 197 Processing sheet with id= O, first strand: chain 'D' and resid 285 through 287 removed outlier: 3.758A pdb=" N GLY D 299 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYR D 293 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 229 through 233 removed outlier: 6.556A pdb=" N GLU D 233 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 257 through 263 removed outlier: 6.283A pdb=" N ARG E 222 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL E 221 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU E 189 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE E 64 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE E 191 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY E 66 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN E 193 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU E 115 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASP E 94 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER E 117 " --> pdb=" O ASP E 94 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 195 through 197 Processing sheet with id= S, first strand: chain 'E' and resid 229 through 233 removed outlier: 3.508A pdb=" N GLY E 229 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU E 233 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 290 through 293 removed outlier: 3.513A pdb=" N GLY E 299 " --> pdb=" O TYR E 291 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR E 293 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LYS E 297 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 257 through 263 removed outlier: 6.344A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU F 189 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE F 64 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE F 191 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY F 66 " --> pdb=" O PHE F 191 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 195 through 197 Processing sheet with id= W, first strand: chain 'F' and resid 229 through 233 removed outlier: 6.605A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 290 through 293 removed outlier: 6.542A pdb=" N TYR F 293 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 257 through 263 removed outlier: 6.329A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL G 221 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU G 189 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE G 64 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE G 191 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLY G 66 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN G 193 " --> pdb=" O GLY G 66 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 195 through 197 Processing sheet with id= AA, first strand: chain 'G' and resid 229 through 233 removed outlier: 6.527A pdb=" N GLU G 233 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 290 through 292 Processing sheet with id= AC, first strand: chain 'H' and resid 257 through 263 removed outlier: 6.428A pdb=" N ARG H 222 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL H 221 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU H 189 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE H 64 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE H 191 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY H 66 " --> pdb=" O PHE H 191 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN H 193 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU H 115 " --> pdb=" O PHE H 92 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 195 through 197 Processing sheet with id= AE, first strand: chain 'H' and resid 229 through 233 removed outlier: 6.470A pdb=" N GLU H 233 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 290 through 293 removed outlier: 6.523A pdb=" N TYR H 293 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS H 297 " --> pdb=" O TYR H 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 257 through 263 removed outlier: 6.499A pdb=" N ARG I 222 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL I 221 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU I 189 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE I 64 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE I 191 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLY I 66 " --> pdb=" O PHE I 191 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN I 193 " --> pdb=" O GLY I 66 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU I 115 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP I 94 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER I 117 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 195 through 197 Processing sheet with id= AI, first strand: chain 'I' and resid 229 through 233 removed outlier: 6.677A pdb=" N GLU I 233 " --> pdb=" O VAL I 237 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL I 237 " --> pdb=" O GLU I 233 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 290 through 293 removed outlier: 6.307A pdb=" N TYR I 293 " --> pdb=" O LYS I 297 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS I 297 " --> pdb=" O TYR I 293 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 16.72 Time building geometry restraints manager: 31.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 23379 1.09 - 1.33: 5544 1.33 - 1.57: 20184 1.57 - 1.81: 376 1.81 - 2.05: 81 Bond restraints: 49564 Sorted by residual: bond pdb=" N1 DG U 8 " pdb=" H1 DG U 8 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" N3 DT T 5 " pdb=" H3 DT T 5 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" N3 DT T 18 " pdb=" H3 DT T 18 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" N3 DT U 35 " pdb=" H3 DT U 35 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" N3 DT U 11 " pdb=" H3 DT U 11 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 ... (remaining 49559 not shown) Histogram of bond angle deviations from ideal: 91.58 - 100.59: 83 100.59 - 109.60: 45279 109.60 - 118.61: 26821 118.61 - 127.62: 17600 127.62 - 136.63: 244 Bond angle restraints: 90027 Sorted by residual: angle pdb=" C5 AGS F 402 " pdb=" C4 AGS F 402 " pdb=" N3 AGS F 402 " ideal model delta sigma weight residual 126.80 116.96 9.84 7.41e-01 1.82e+00 1.76e+02 angle pdb=" C5 AGS H 402 " pdb=" C4 AGS H 402 " pdb=" N3 AGS H 402 " ideal model delta sigma weight residual 126.80 117.99 8.81 7.41e-01 1.82e+00 1.41e+02 angle pdb=" C5 AGS C 402 " pdb=" C4 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 126.80 118.45 8.35 7.41e-01 1.82e+00 1.27e+02 angle pdb=" C5 AGS D 402 " pdb=" C4 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 126.80 118.47 8.33 7.41e-01 1.82e+00 1.26e+02 angle pdb=" C5 AGS I 402 " pdb=" C4 AGS I 402 " pdb=" N3 AGS I 402 " ideal model delta sigma weight residual 126.80 118.48 8.32 7.41e-01 1.82e+00 1.26e+02 ... (remaining 90022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 20989 34.50 - 69.00: 1538 69.00 - 103.50: 45 103.50 - 138.00: 2 138.00 - 172.49: 9 Dihedral angle restraints: 22583 sinusoidal: 13454 harmonic: 9129 Sorted by residual: dihedral pdb=" CA SER C 145 " pdb=" C SER C 145 " pdb=" N VAL C 146 " pdb=" CA VAL C 146 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA SER F 145 " pdb=" C SER F 145 " pdb=" N VAL F 146 " pdb=" CA VAL F 146 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA SER E 145 " pdb=" C SER E 145 " pdb=" N VAL E 146 " pdb=" CA VAL E 146 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 22580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2434 0.079 - 0.158: 1254 0.158 - 0.238: 281 0.238 - 0.317: 17 0.317 - 0.396: 5 Chirality restraints: 3991 Sorted by residual: chirality pdb=" CA SER F 145 " pdb=" N SER F 145 " pdb=" C SER F 145 " pdb=" CB SER F 145 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C2' AGS H 402 " pdb=" C1' AGS H 402 " pdb=" C3' AGS H 402 " pdb=" O2' AGS H 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.32 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA SER E 145 " pdb=" N SER E 145 " pdb=" C SER E 145 " pdb=" CB SER E 145 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 3988 not shown) Planarity restraints: 7028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA S 21 " -0.063 2.00e-02 2.50e+03 2.44e-02 1.93e+01 pdb=" N9 DA S 21 " 0.046 2.00e-02 2.50e+03 pdb=" C8 DA S 21 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA S 21 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA S 21 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DA S 21 " -0.013 2.00e-02 2.50e+03 pdb=" N6 DA S 21 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DA S 21 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DA S 21 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA S 21 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DA S 21 " 0.019 2.00e-02 2.50e+03 pdb=" H8 DA S 21 " -0.003 2.00e-02 2.50e+03 pdb=" H2 DA S 21 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA S 15 " -0.057 2.00e-02 2.50e+03 2.29e-02 1.70e+01 pdb=" N9 DA S 15 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DA S 15 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DA S 15 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DA S 15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA S 15 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA S 15 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DA S 15 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DA S 15 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA S 15 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DA S 15 " 0.010 2.00e-02 2.50e+03 pdb=" H8 DA S 15 " 0.001 2.00e-02 2.50e+03 pdb=" H2 DA S 15 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA S 19 " 0.054 2.00e-02 2.50e+03 1.96e-02 1.25e+01 pdb=" N9 DA S 19 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA S 19 " -0.013 2.00e-02 2.50e+03 pdb=" N7 DA S 19 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA S 19 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA S 19 " 0.022 2.00e-02 2.50e+03 pdb=" N6 DA S 19 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DA S 19 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA S 19 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA S 19 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DA S 19 " -0.010 2.00e-02 2.50e+03 pdb=" H8 DA S 19 " -0.012 2.00e-02 2.50e+03 pdb=" H2 DA S 19 " -0.010 2.00e-02 2.50e+03 ... (remaining 7025 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 533 2.03 - 2.67: 62041 2.67 - 3.31: 140896 3.31 - 3.96: 186542 3.96 - 4.60: 284268 Nonbonded interactions: 674280 Sorted by model distance: nonbonded pdb="HH11 ARG G 60 " pdb=" HG SER G 220 " model vdw 1.382 2.100 nonbonded pdb="HH11 ARG D 60 " pdb=" HG SER D 220 " model vdw 1.481 2.100 nonbonded pdb="HH11 ARG C 60 " pdb=" HG SER C 220 " model vdw 1.517 2.100 nonbonded pdb="HH11 ARG E 60 " pdb=" HG SER E 220 " model vdw 1.564 2.100 nonbonded pdb=" H GLY F 122 " pdb=" O THR F 150 " model vdw 1.577 1.850 ... (remaining 674275 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 34 through 333 or resid 401 through 402)) selection = (chain 'B' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'C' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'D' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'E' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'F' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'G' and (resid 34 through 333 or resid 401 through 402)) selection = (chain 'H' and (resid 34 through 333 or resid 401 through 402)) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.440 Construct map_model_manager: 0.520 Extract box with map and model: 5.410 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 132.570 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.130 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:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 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 : 0.014 0.125 25381 Z= 0.895 Angle : 1.917 14.387 34697 Z= 1.399 Chirality : 0.090 0.396 3991 Planarity : 0.005 0.027 4071 Dihedral : 20.652 172.495 9949 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.99 % Favored : 96.71 % Rotamer: Outliers : 5.31 % Allowed : 8.95 % Favored : 85.73 % Cbeta Deviations : 0.04 % 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: -2.59 (0.13), residues: 2946 helix: -1.91 (0.11), residues: 1285 sheet: 0.42 (0.22), residues: 484 loop : -2.31 (0.15), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 308 HIS 0.009 0.003 HIS C 97 PHE 0.035 0.004 PHE D 255 TYR 0.031 0.004 TYR G 65 ARG 0.013 0.002 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 436 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PRO cc_start: 0.6745 (Cg_endo) cc_final: 0.6459 (Cg_exo) REVERT: A 127 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6594 (tp30) REVERT: B 245 LYS cc_start: 0.8311 (mttp) cc_final: 0.8053 (mmmt) REVERT: C 152 LYS cc_start: 0.7743 (tttm) cc_final: 0.7394 (mttt) REVERT: C 245 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8066 (tmtm) REVERT: C 309 LEU cc_start: 0.7527 (mt) cc_final: 0.7213 (tp) REVERT: D 8 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7993 (mmtm) REVERT: D 18 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7066 (mt-10) REVERT: D 96 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7629 (mt-10) REVERT: G 171 MET cc_start: 0.8476 (mmm) cc_final: 0.8108 (mmm) REVERT: H 74 THR cc_start: 0.5777 (OUTLIER) cc_final: 0.5412 (m) REVERT: H 175 MET cc_start: 0.5440 (mmp) cc_final: 0.5224 (mmp) outliers start: 124 outliers final: 34 residues processed: 544 average time/residue: 2.0980 time to fit residues: 1343.0803 Evaluate side-chains 296 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 254 PRO Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 254 PRO Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 297 LYS Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 155 optimal weight: 0.0040 chunk 123 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 205 ASN A 332 ASN B 20 GLN C 16 GLN D 304 ASN E 300 GLN F 113 ASN F 184 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25381 Z= 0.198 Angle : 0.594 5.870 34697 Z= 0.333 Chirality : 0.042 0.166 3991 Planarity : 0.004 0.032 4071 Dihedral : 20.874 177.883 4613 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.46 % Favored : 98.30 % Rotamer: Outliers : 2.83 % Allowed : 16.80 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 2946 helix: 0.54 (0.14), residues: 1301 sheet: 0.72 (0.22), residues: 504 loop : -1.97 (0.16), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 308 HIS 0.004 0.001 HIS F 97 PHE 0.011 0.001 PHE H 191 TYR 0.009 0.001 TYR G 271 ARG 0.004 0.001 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 291 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PRO cc_start: 0.6474 (Cg_endo) cc_final: 0.6242 (Cg_exo) REVERT: A 259 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6768 (mt-10) REVERT: A 326 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5705 (mt) REVERT: B 245 LYS cc_start: 0.8241 (mttp) cc_final: 0.8015 (mtpp) REVERT: C 152 LYS cc_start: 0.7958 (tttm) cc_final: 0.7648 (mttt) REVERT: C 309 LEU cc_start: 0.7674 (mt) cc_final: 0.7355 (tp) REVERT: D 8 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7874 (mppt) REVERT: D 16 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7824 (tm-30) REVERT: D 18 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6984 (mt-10) REVERT: D 96 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7616 (mt-10) REVERT: D 202 MET cc_start: 0.5306 (mtm) cc_final: 0.5092 (mtm) REVERT: F 86 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: G 171 MET cc_start: 0.8411 (mmm) cc_final: 0.8042 (mmm) REVERT: G 241 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: H 202 MET cc_start: 0.2685 (mpt) cc_final: 0.2005 (ttt) REVERT: I 224 ASP cc_start: 0.5834 (t70) cc_final: 0.5591 (t70) REVERT: I 247 VAL cc_start: 0.5071 (p) cc_final: 0.4846 (t) outliers start: 66 outliers final: 29 residues processed: 347 average time/residue: 2.2743 time to fit residues: 926.1921 Evaluate side-chains 298 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 265 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 297 LYS Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 276 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 chunk 246 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN D 304 ASN F 118 GLN G 184 GLN G 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25381 Z= 0.208 Angle : 0.552 7.370 34697 Z= 0.305 Chirality : 0.043 0.178 3991 Planarity : 0.004 0.036 4071 Dihedral : 20.521 173.815 4578 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.79 % Rotamer: Outliers : 2.53 % Allowed : 17.91 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2946 helix: 1.44 (0.14), residues: 1293 sheet: 0.88 (0.22), residues: 498 loop : -1.86 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 308 HIS 0.005 0.001 HIS D 97 PHE 0.012 0.001 PHE A 270 TYR 0.016 0.001 TYR H 218 ARG 0.004 0.000 ARG D 196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 273 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: B 245 LYS cc_start: 0.8255 (mttp) cc_final: 0.8045 (mtpp) REVERT: C 152 LYS cc_start: 0.8055 (tttm) cc_final: 0.7634 (mttt) REVERT: C 309 LEU cc_start: 0.7689 (mt) cc_final: 0.7389 (tp) REVERT: D 96 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7617 (mt-10) REVERT: E 154 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: F 86 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: F 245 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8125 (mttt) REVERT: F 266 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: G 127 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7049 (mm-30) REVERT: G 171 MET cc_start: 0.8438 (mmm) cc_final: 0.8050 (mmm) REVERT: I 35 MET cc_start: 0.4971 (mmt) cc_final: 0.4719 (mpt) REVERT: I 58 MET cc_start: 0.5482 (OUTLIER) cc_final: 0.4671 (mmt) outliers start: 59 outliers final: 29 residues processed: 316 average time/residue: 2.3177 time to fit residues: 849.8969 Evaluate side-chains 292 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 257 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 277 optimal weight: 20.0000 chunk 293 optimal weight: 0.1980 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN G 184 GLN I 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25381 Z= 0.300 Angle : 0.597 9.454 34697 Z= 0.325 Chirality : 0.045 0.232 3991 Planarity : 0.004 0.047 4071 Dihedral : 20.333 171.634 4565 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 3.04 % Allowed : 18.21 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2946 helix: 1.37 (0.14), residues: 1285 sheet: 0.78 (0.22), residues: 494 loop : -1.82 (0.15), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 308 HIS 0.009 0.002 HIS D 97 PHE 0.013 0.002 PHE D 255 TYR 0.014 0.002 TYR F 291 ARG 0.005 0.001 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 263 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6900 (mt-10) REVERT: C 152 LYS cc_start: 0.8031 (tttm) cc_final: 0.7540 (mttt) REVERT: C 158 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7428 (mm-30) REVERT: C 309 LEU cc_start: 0.7766 (mt) cc_final: 0.7472 (tp) REVERT: D 4 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5912 (tt0) REVERT: D 96 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7769 (mt-10) REVERT: E 154 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: F 86 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: F 256 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7574 (mtpt) REVERT: F 266 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: G 171 MET cc_start: 0.8493 (mmm) cc_final: 0.8053 (mmm) REVERT: H 123 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.6010 (pp20) REVERT: I 58 MET cc_start: 0.5635 (OUTLIER) cc_final: 0.4993 (mmt) outliers start: 71 outliers final: 35 residues processed: 320 average time/residue: 2.2963 time to fit residues: 854.4891 Evaluate side-chains 294 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 251 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 256 LYS Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain I residue 58 MET Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 218 optimal weight: 0.0050 chunk 121 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 74 optimal weight: 0.0870 overall best weight: 1.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN D 304 ASN D 312 ASN G 184 GLN I 118 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25381 Z= 0.186 Angle : 0.512 7.531 34697 Z= 0.284 Chirality : 0.042 0.160 3991 Planarity : 0.003 0.046 4071 Dihedral : 20.180 169.432 4562 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.36 % Allowed : 19.41 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 2946 helix: 1.73 (0.15), residues: 1285 sheet: 0.81 (0.22), residues: 494 loop : -1.69 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 308 HIS 0.004 0.001 HIS D 97 PHE 0.009 0.001 PHE I 191 TYR 0.015 0.001 TYR F 291 ARG 0.002 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 260 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6927 (mpp) REVERT: C 152 LYS cc_start: 0.8093 (tttm) cc_final: 0.7569 (mttt) REVERT: C 158 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 309 LEU cc_start: 0.7725 (mt) cc_final: 0.7463 (tp) REVERT: D 96 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7598 (mt-10) REVERT: E 86 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: E 154 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: F 86 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: F 266 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: G 171 MET cc_start: 0.8489 (mmm) cc_final: 0.8067 (mmm) REVERT: H 123 GLU cc_start: 0.6384 (pp20) cc_final: 0.5973 (pp20) REVERT: H 202 MET cc_start: 0.2791 (OUTLIER) cc_final: 0.1586 (mmm) REVERT: H 233 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5151 (pt0) REVERT: I 178 LEU cc_start: 0.4602 (OUTLIER) cc_final: 0.4320 (tt) outliers start: 55 outliers final: 32 residues processed: 300 average time/residue: 2.2420 time to fit residues: 785.5992 Evaluate side-chains 285 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 202 MET Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN D 304 ASN G 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25381 Z= 0.192 Angle : 0.508 7.210 34697 Z= 0.281 Chirality : 0.042 0.155 3991 Planarity : 0.003 0.043 4071 Dihedral : 20.009 170.526 4561 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.49 % Allowed : 19.19 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2946 helix: 2.05 (0.15), residues: 1238 sheet: 0.82 (0.22), residues: 494 loop : -1.45 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 308 HIS 0.004 0.001 HIS F 97 PHE 0.012 0.001 PHE A 270 TYR 0.022 0.001 TYR F 291 ARG 0.004 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 257 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: C 152 LYS cc_start: 0.8108 (tttm) cc_final: 0.7607 (mttt) REVERT: C 309 LEU cc_start: 0.7738 (mt) cc_final: 0.7446 (tp) REVERT: D 96 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7620 (mt-10) REVERT: E 86 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: E 120 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: E 154 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: G 171 MET cc_start: 0.8518 (mmm) cc_final: 0.8088 (mmm) REVERT: H 123 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5889 (pp20) REVERT: H 202 MET cc_start: 0.2969 (OUTLIER) cc_final: 0.1777 (mmm) REVERT: H 233 GLU cc_start: 0.5789 (OUTLIER) cc_final: 0.5137 (pt0) REVERT: I 178 LEU cc_start: 0.4544 (OUTLIER) cc_final: 0.4277 (tt) outliers start: 58 outliers final: 35 residues processed: 305 average time/residue: 2.2707 time to fit residues: 807.4558 Evaluate side-chains 291 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 202 MET Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN D 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25381 Z= 0.305 Angle : 0.581 8.714 34697 Z= 0.315 Chirality : 0.045 0.223 3991 Planarity : 0.004 0.049 4071 Dihedral : 20.063 171.687 4558 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.00 % Allowed : 18.98 % Favored : 78.02 % 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: 0.40 (0.15), residues: 2946 helix: 1.71 (0.15), residues: 1238 sheet: 0.77 (0.22), residues: 493 loop : -1.55 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 308 HIS 0.006 0.001 HIS F 97 PHE 0.014 0.002 PHE D 255 TYR 0.020 0.001 TYR F 291 ARG 0.004 0.001 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 255 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: A 310 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6302 (tppp) REVERT: B 63 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: C 8 LYS cc_start: 0.8386 (mttt) cc_final: 0.8153 (mttt) REVERT: C 152 LYS cc_start: 0.7987 (tttm) cc_final: 0.7547 (mttt) REVERT: C 309 LEU cc_start: 0.7746 (mt) cc_final: 0.7508 (tp) REVERT: D 96 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7785 (mt-10) REVERT: D 164 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7265 (ttm) REVERT: E 86 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: E 154 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: F 266 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: G 161 ASP cc_start: 0.8005 (m-30) cc_final: 0.7675 (m-30) REVERT: G 171 MET cc_start: 0.8501 (mmm) cc_final: 0.8034 (mmm) REVERT: G 241 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: H 123 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5978 (pp20) REVERT: H 233 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5249 (pt0) REVERT: I 178 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4321 (tt) outliers start: 70 outliers final: 41 residues processed: 307 average time/residue: 2.2614 time to fit residues: 810.5618 Evaluate side-chains 296 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 244 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 238 VAL Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 202 MET Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN D 304 ASN G 184 GLN G 186 ASN I 118 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25381 Z= 0.200 Angle : 0.519 8.259 34697 Z= 0.285 Chirality : 0.042 0.154 3991 Planarity : 0.003 0.046 4071 Dihedral : 19.942 169.719 4558 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.66 % Allowed : 19.79 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 2946 helix: 1.95 (0.15), residues: 1238 sheet: 0.78 (0.22), residues: 493 loop : -1.46 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 308 HIS 0.004 0.001 HIS F 97 PHE 0.009 0.001 PHE A 270 TYR 0.017 0.001 TYR F 291 ARG 0.002 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 247 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6938 (mpp) REVERT: A 310 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6325 (tppp) REVERT: C 152 LYS cc_start: 0.8000 (tttm) cc_final: 0.7551 (mttt) REVERT: C 309 LEU cc_start: 0.7733 (mt) cc_final: 0.7529 (tp) REVERT: D 96 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7691 (mt-10) REVERT: E 86 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: E 154 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: E 226 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8691 (mtp85) REVERT: G 161 ASP cc_start: 0.7989 (m-30) cc_final: 0.7638 (m-30) REVERT: G 171 MET cc_start: 0.8519 (mmm) cc_final: 0.8062 (mmm) REVERT: G 241 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: H 123 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5942 (pp20) REVERT: H 233 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5149 (pt0) REVERT: I 178 LEU cc_start: 0.4514 (OUTLIER) cc_final: 0.4250 (tt) outliers start: 62 outliers final: 38 residues processed: 294 average time/residue: 2.3055 time to fit residues: 797.1333 Evaluate side-chains 289 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 242 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 202 MET Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 GLN D 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25381 Z= 0.386 Angle : 0.634 9.506 34697 Z= 0.340 Chirality : 0.047 0.269 3991 Planarity : 0.005 0.050 4071 Dihedral : 20.034 171.296 4557 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.84 % Rotamer: Outliers : 2.78 % Allowed : 19.92 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2946 helix: 1.47 (0.15), residues: 1237 sheet: 0.69 (0.22), residues: 493 loop : -1.62 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 308 HIS 0.008 0.002 HIS F 97 PHE 0.018 0.002 PHE D 255 TYR 0.020 0.002 TYR F 291 ARG 0.005 0.001 ARG E 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 251 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6324 (tppp) REVERT: B 309 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6684 (tm) REVERT: C 152 LYS cc_start: 0.7991 (tttm) cc_final: 0.7532 (mttt) REVERT: C 309 LEU cc_start: 0.7805 (mt) cc_final: 0.7574 (tp) REVERT: D 164 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7261 (ttm) REVERT: E 86 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: E 154 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: E 226 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8722 (mtp85) REVERT: E 328 LEU cc_start: 0.4568 (OUTLIER) cc_final: 0.4323 (mm) REVERT: F 266 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: G 171 MET cc_start: 0.8515 (mmm) cc_final: 0.8034 (mmm) REVERT: G 241 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: H 123 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6081 (pp20) REVERT: H 172 SER cc_start: 0.5804 (OUTLIER) cc_final: 0.5425 (t) REVERT: H 233 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5326 (pt0) REVERT: I 178 LEU cc_start: 0.4523 (OUTLIER) cc_final: 0.4268 (tt) REVERT: I 202 MET cc_start: 0.1693 (tmm) cc_final: 0.1214 (tmm) outliers start: 65 outliers final: 36 residues processed: 298 average time/residue: 2.3661 time to fit residues: 826.1807 Evaluate side-chains 292 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 243 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 1.9990 chunk 288 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 200 optimal weight: 8.9990 chunk 302 optimal weight: 8.9990 chunk 278 optimal weight: 20.0000 chunk 241 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 147 optimal weight: 0.0370 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN D 304 ASN G 184 GLN I 118 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25381 Z= 0.153 Angle : 0.499 8.102 34697 Z= 0.277 Chirality : 0.042 0.153 3991 Planarity : 0.003 0.042 4071 Dihedral : 19.885 166.722 4557 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.46 % Allowed : 21.55 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 2946 helix: 2.02 (0.15), residues: 1237 sheet: 0.78 (0.22), residues: 493 loop : -1.41 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 308 HIS 0.004 0.001 HIS D 97 PHE 0.011 0.001 PHE A 270 TYR 0.015 0.001 TYR B 291 ARG 0.002 0.000 ARG E 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 253 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6292 (tppp) REVERT: C 152 LYS cc_start: 0.8040 (tttm) cc_final: 0.7494 (mttt) REVERT: E 154 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: E 226 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8665 (mtp85) REVERT: G 161 ASP cc_start: 0.8069 (m-30) cc_final: 0.7701 (m-30) REVERT: G 171 MET cc_start: 0.8537 (mmm) cc_final: 0.8075 (mmm) REVERT: G 241 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: H 123 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6038 (pp20) REVERT: H 233 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5116 (pt0) REVERT: I 178 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4189 (tt) outliers start: 34 outliers final: 24 residues processed: 282 average time/residue: 2.4273 time to fit residues: 800.6999 Evaluate side-chains 271 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 226 ARG Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 134 ARG Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 224 ASP Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 0.1980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN C 118 GLN D 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.210344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162467 restraints weight = 67495.913| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.05 r_work: 0.3489 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25381 Z= 0.180 Angle : 0.508 10.254 34697 Z= 0.279 Chirality : 0.042 0.150 3991 Planarity : 0.003 0.042 4071 Dihedral : 19.764 170.866 4557 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.50 % Allowed : 21.51 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 2946 helix: 2.14 (0.15), residues: 1237 sheet: 0.84 (0.22), residues: 499 loop : -1.35 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 308 HIS 0.004 0.001 HIS F 97 PHE 0.018 0.001 PHE A 270 TYR 0.016 0.001 TYR B 291 ARG 0.002 0.000 ARG B 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13960.46 seconds wall clock time: 240 minutes 42.16 seconds (14442.16 seconds total)