Starting phenix.real_space_refine on Sat May 11 15:15:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/05_2024/8xn4_38497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/05_2024/8xn4_38497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/05_2024/8xn4_38497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/05_2024/8xn4_38497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/05_2024/8xn4_38497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/05_2024/8xn4_38497.pdb" } resolution = 2.34 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= 0.009 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12026 2.51 5 N 3269 2.21 5 O 3766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C ASP 55": "OD1" <-> "OD2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D ASP 185": "OD1" <-> "OD2" Residue "D ASP 187": "OD1" <-> "OD2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "E ASP 203": "OD1" <-> "OD2" Residue "F ASP 74": "OD1" <-> "OD2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 202": "OD1" <-> "OD2" Residue "F ASP 203": "OD1" <-> "OD2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 183": "OD1" <-> "OD2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H ASP 112": "OD1" <-> "OD2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H ASP 186": "OD1" <-> "OD2" Residue "H GLU 201": "OE1" <-> "OE2" Residue "H ASP 206": "OD1" <-> "OD2" Residue "H TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 52": "OD1" <-> "OD2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I ASP 112": "OD1" <-> "OD2" Residue "I TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 120": "OD1" <-> "OD2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I ASP 186": "OD1" <-> "OD2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "I ASP 206": "OD1" <-> "OD2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 176": "OE1" <-> "OE2" Residue "J ASP 186": "OD1" <-> "OD2" Residue "J ARG 205": "NH1" <-> "NH2" Residue "J ASP 213": "OD1" <-> "OD2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K ASP 76": "OD1" <-> "OD2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "K ASP 169": "OD1" <-> "OD2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K ASP 186": "OD1" <-> "OD2" Residue "K ASP 202": "OD1" <-> "OD2" Residue "K ASP 206": "OD1" <-> "OD2" Residue "K ASP 213": "OD1" <-> "OD2" Residue "K ASP 221": "OD1" <-> "OD2" Residue "L ASP 90": "OD1" <-> "OD2" Residue "L ASP 112": "OD1" <-> "OD2" Residue "L ASP 120": "OD1" <-> "OD2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 186": "OD1" <-> "OD2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "L ASP 202": "OD1" <-> "OD2" Residue "L TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 221": "OD1" <-> "OD2" Residue "M GLU 60": "OE1" <-> "OE2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M ASP 112": "OD1" <-> "OD2" Residue "M ASP 120": "OD1" <-> "OD2" Residue "M GLU 176": "OE1" <-> "OE2" Residue "M ASP 186": "OD1" <-> "OD2" Residue "M GLU 201": "OE1" <-> "OE2" Residue "M ASP 202": "OD1" <-> "OD2" Residue "M TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N ASP 88": "OD1" <-> "OD2" Residue "N ASP 92": "OD1" <-> "OD2" Residue "N PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 112": "OD1" <-> "OD2" Residue "N GLU 185": "OE1" <-> "OE2" Residue "N ASP 186": "OD1" <-> "OD2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N GLU 204": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 19173 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "D" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "F" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "G" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1393 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "H" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "L" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "M" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "N" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1346 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Time building chain proxies: 10.48, per 1000 atoms: 0.55 Number of scatterers: 19173 At special positions: 0 Unit cell: (115.92, 115.92, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3766 8.00 N 3269 7.00 C 12026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.61 Conformation dependent library (CDL) restraints added in 4.1 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 41 sheets defined 53.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.719A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.637A pdb=" N LYS A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 148 through 174 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 85 through 99 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 149 through 174 removed outlier: 3.572A pdb=" N ILE C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 148 through 174 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 191 through 199 Processing helix chain 'D' and resid 207 through 211 removed outlier: 3.515A pdb=" N MET D 211 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.678A pdb=" N GLY E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 removed outlier: 3.738A pdb=" N PHE E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 174 Processing helix chain 'E' and resid 176 through 185 removed outlier: 3.528A pdb=" N ILE E 180 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 85 through 99 Processing helix chain 'F' and resid 113 through 121 removed outlier: 3.652A pdb=" N PHE F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 174 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 191 through 199 Processing helix chain 'F' and resid 207 through 211 removed outlier: 3.595A pdb=" N MET F 211 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 42 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.606A pdb=" N GLY G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 removed outlier: 3.709A pdb=" N PHE G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 174 Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 191 through 199 Processing helix chain 'H' and resid 53 through 60 Processing helix chain 'H' and resid 70 through 87 removed outlier: 3.557A pdb=" N MET H 87 " --> pdb=" O CYS H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.503A pdb=" N LEU H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 167 through 191 Processing helix chain 'H' and resid 195 through 203 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 53 through 60 Processing helix chain 'I' and resid 70 through 87 Processing helix chain 'I' and resid 103 through 117 Processing helix chain 'I' and resid 131 through 138 Processing helix chain 'I' and resid 167 through 192 Processing helix chain 'I' and resid 195 through 203 Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 70 through 87 removed outlier: 3.546A pdb=" N MET J 87 " --> pdb=" O CYS J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 117 Processing helix chain 'J' and resid 130 through 138 Processing helix chain 'J' and resid 167 through 193 Processing helix chain 'J' and resid 195 through 202 Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'K' and resid 53 through 60 Processing helix chain 'K' and resid 70 through 88 removed outlier: 3.819A pdb=" N MET K 87 " --> pdb=" O CYS K 83 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 117 Processing helix chain 'K' and resid 131 through 138 Processing helix chain 'K' and resid 167 through 191 Processing helix chain 'K' and resid 195 through 204 Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 53 through 60 Processing helix chain 'L' and resid 70 through 87 Processing helix chain 'L' and resid 103 through 117 Processing helix chain 'L' and resid 130 through 138 Processing helix chain 'L' and resid 166 through 191 removed outlier: 3.642A pdb=" N LEU L 170 " --> pdb=" O GLN L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 203 Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'M' and resid 53 through 60 removed outlier: 3.502A pdb=" N GLU M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 87 Processing helix chain 'M' and resid 103 through 117 removed outlier: 3.540A pdb=" N LEU M 107 " --> pdb=" O SER M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 138 Processing helix chain 'M' and resid 167 through 192 Processing helix chain 'M' and resid 195 through 204 removed outlier: 3.535A pdb=" N GLU M 204 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'N' and resid 53 through 60 Processing helix chain 'N' and resid 70 through 87 removed outlier: 3.736A pdb=" N MET N 87 " --> pdb=" O CYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 117 Processing helix chain 'N' and resid 131 through 138 Processing helix chain 'N' and resid 167 through 192 Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.601A pdb=" N GLU N 204 " --> pdb=" O ARG N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.031A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 134 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY A 109 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU A 136 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA A 111 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 188 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.031A pdb=" N ILE A 46 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN A 80 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 48 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 75 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 106 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 77 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET A 108 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 79 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU A 110 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N PHE A 128 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR A 105 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.476A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B 134 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY B 109 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 136 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 111 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 188 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 5.476A pdb=" N SER B 81 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 110 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE B 128 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 105 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.559A pdb=" N ALA B 142 " --> pdb=" O GLY J 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY J 165 " --> pdb=" O ALA B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.717A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE C 106 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 77 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 108 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 79 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 110 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.717A pdb=" N ILE C 46 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN C 80 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 48 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE C 106 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 77 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET C 108 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 79 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 110 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE C 128 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR C 105 " --> pdb=" O PHE C 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.525A pdb=" N GLY K 165 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.713A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 75 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 106 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 77 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET D 108 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE D 79 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU D 110 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU D 134 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY D 109 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU D 136 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA D 111 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.713A pdb=" N ILE D 46 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN D 80 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 48 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 75 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 106 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 77 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET D 108 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE D 79 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU D 110 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 128 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR D 105 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.367A pdb=" N ILE E 75 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE E 106 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 77 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET E 108 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE E 79 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU E 110 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU E 134 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY E 109 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU E 136 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA E 111 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.367A pdb=" N ILE E 75 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE E 106 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 77 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET E 108 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE E 79 " --> pdb=" O MET E 108 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU E 110 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N PHE E 128 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR E 105 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.507A pdb=" N ALA E 142 " --> pdb=" O GLY M 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY M 165 " --> pdb=" O ALA E 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.469A pdb=" N ILE F 75 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE F 106 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 77 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET F 108 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE F 79 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU F 110 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU F 134 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY F 109 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 136 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA F 111 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 188 " --> pdb=" O ILE F 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.469A pdb=" N ILE F 75 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE F 106 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 77 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET F 108 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE F 79 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU F 110 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE F 128 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR F 105 " --> pdb=" O PHE F 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AC5, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC6, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.695A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.695A pdb=" N ILE G 46 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN G 80 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU G 48 " --> pdb=" O ASN G 80 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER G 81 " --> pdb=" O MET G 108 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU G 110 " --> pdb=" O SER G 81 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N PHE G 128 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR G 105 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AC9, first strand: chain 'G' and resid 146 through 147 Processing sheet with id=AD1, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.423A pdb=" N ILE H 93 " --> pdb=" O GLN H 122 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL H 124 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL H 95 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET H 126 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE H 97 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN H 128 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 99 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ARG H 152 " --> pdb=" O CYS H 125 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY H 127 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LEU H 154 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA H 129 " --> pdb=" O LEU H 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 62 through 65 removed outlier: 6.423A pdb=" N ILE H 93 " --> pdb=" O GLN H 122 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL H 124 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL H 95 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N MET H 126 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE H 97 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN H 128 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 99 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N MET H 146 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR H 123 " --> pdb=" O MET H 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 62 through 65 removed outlier: 5.465A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG I 152 " --> pdb=" O GLY I 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 62 through 65 removed outlier: 5.465A pdb=" N SER I 99 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN I 128 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N MET I 146 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR I 123 " --> pdb=" O MET I 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.332A pdb=" N ILE J 93 " --> pdb=" O GLN J 122 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL J 124 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL J 95 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET J 126 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE J 97 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN J 128 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG J 152 " --> pdb=" O CYS J 125 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY J 127 " --> pdb=" O ARG J 152 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LEU J 154 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA J 129 " --> pdb=" O LEU J 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.332A pdb=" N ILE J 93 " --> pdb=" O GLN J 122 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL J 124 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL J 95 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET J 126 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE J 97 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN J 128 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN J 222 " --> pdb=" O ARG J 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.579A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG K 152 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.579A pdb=" N SER K 99 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN K 128 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET K 146 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR K 123 " --> pdb=" O MET K 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.187A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET L 126 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE L 97 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN L 128 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG L 152 " --> pdb=" O CYS L 125 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY L 127 " --> pdb=" O ARG L 152 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N LEU L 154 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA L 129 " --> pdb=" O LEU L 154 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 62 through 65 removed outlier: 6.187A pdb=" N ILE L 93 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET L 126 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE L 97 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLN L 128 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG L 145 " --> pdb=" O GLN L 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.781A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE M 93 " --> pdb=" O GLN M 122 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL M 124 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL M 95 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N MET M 126 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE M 97 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN M 128 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS M 207 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.781A pdb=" N ILE M 63 " --> pdb=" O TYR M 96 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASN M 98 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU M 65 " --> pdb=" O ASN M 98 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE M 93 " --> pdb=" O GLN M 122 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL M 124 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL M 95 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N MET M 126 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE M 97 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN M 128 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N MET M 146 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR M 123 " --> pdb=" O MET M 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.846A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.846A pdb=" N ILE N 63 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN N 98 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU N 65 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE N 93 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL N 124 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL N 95 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET N 126 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE N 97 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN N 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.70 Time building geometry restraints manager: 8.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3387 1.30 - 1.43: 4415 1.43 - 1.56: 11448 1.56 - 1.69: 0 1.69 - 1.82: 210 Bond restraints: 19460 Sorted by residual: bond pdb=" CA SER L 160 " pdb=" CB SER L 160 " ideal model delta sigma weight residual 1.530 1.451 0.079 1.36e-02 5.41e+03 3.41e+01 bond pdb=" C ASP E 185 " pdb=" O ASP E 185 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.26e-02 6.30e+03 3.13e+01 bond pdb=" C GLU E 178 " pdb=" O GLU E 178 " ideal model delta sigma weight residual 1.237 1.297 -0.061 1.16e-02 7.43e+03 2.75e+01 bond pdb=" C THR E 181 " pdb=" O THR E 181 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.16e-02 7.43e+03 2.06e+01 bond pdb=" C PRO J 119 " pdb=" O PRO J 119 " ideal model delta sigma weight residual 1.233 1.182 0.051 1.19e-02 7.06e+03 1.84e+01 ... (remaining 19455 not shown) Histogram of bond angle deviations from ideal: 96.28 - 103.88: 318 103.88 - 111.49: 8753 111.49 - 119.09: 7294 119.09 - 126.70: 9865 126.70 - 134.30: 139 Bond angle restraints: 26369 Sorted by residual: angle pdb=" C THR K 108 " pdb=" CA THR K 108 " pdb=" CB THR K 108 " ideal model delta sigma weight residual 109.95 122.12 -12.17 1.99e+00 2.53e-01 3.74e+01 angle pdb=" N THR K 108 " pdb=" CA THR K 108 " pdb=" C THR K 108 " ideal model delta sigma weight residual 113.18 106.02 7.16 1.21e+00 6.83e-01 3.50e+01 angle pdb=" C THR K 194 " pdb=" CA THR K 194 " pdb=" CB THR K 194 " ideal model delta sigma weight residual 108.86 117.06 -8.20 1.44e+00 4.82e-01 3.24e+01 angle pdb=" C THR J 194 " pdb=" CA THR J 194 " pdb=" CB THR J 194 " ideal model delta sigma weight residual 109.37 118.08 -8.71 1.59e+00 3.96e-01 3.00e+01 angle pdb=" C ALA C 113 " pdb=" CA ALA C 113 " pdb=" CB ALA C 113 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 ... (remaining 26364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10202 17.98 - 35.97: 1240 35.97 - 53.95: 384 53.95 - 71.93: 84 71.93 - 89.91: 39 Dihedral angle restraints: 11949 sinusoidal: 4697 harmonic: 7252 Sorted by residual: dihedral pdb=" CA GLU A 43 " pdb=" C GLU A 43 " pdb=" N ARG A 44 " pdb=" CA ARG A 44 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" C THR K 108 " pdb=" N THR K 108 " pdb=" CA THR K 108 " pdb=" CB THR K 108 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" CA MET J 87 " pdb=" C MET J 87 " pdb=" N ASP J 88 " pdb=" CA ASP J 88 " ideal model delta harmonic sigma weight residual -180.00 -158.31 -21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 11946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2592 0.063 - 0.127: 430 0.127 - 0.190: 44 0.190 - 0.253: 5 0.253 - 0.317: 2 Chirality restraints: 3073 Sorted by residual: chirality pdb=" CB VAL N 117 " pdb=" CA VAL N 117 " pdb=" CG1 VAL N 117 " pdb=" CG2 VAL N 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR K 108 " pdb=" N THR K 108 " pdb=" C THR K 108 " pdb=" CB THR K 108 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA VAL N 117 " pdb=" N VAL N 117 " pdb=" C VAL N 117 " pdb=" CB VAL N 117 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 3070 not shown) Planarity restraints: 3451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS K 191 " 0.022 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C HIS K 191 " -0.074 2.00e-02 2.50e+03 pdb=" O HIS K 191 " 0.026 2.00e-02 2.50e+03 pdb=" N SER K 192 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 70 " 0.061 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO F 71 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 71 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 71 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 70 " 0.061 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO D 71 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 71 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 71 " 0.050 5.00e-02 4.00e+02 ... (remaining 3448 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1829 2.74 - 3.28: 18769 3.28 - 3.82: 31384 3.82 - 4.36: 35858 4.36 - 4.90: 63556 Nonbonded interactions: 151396 Sorted by model distance: nonbonded pdb=" OE1 GLN L 222 " pdb=" N VAL L 223 " model vdw 2.200 2.520 nonbonded pdb=" OD2 ASP I 202 " pdb=" OH TYR I 217 " model vdw 2.205 2.440 nonbonded pdb=" O GLU L 171 " pdb=" ND2 ASN L 175 " model vdw 2.211 2.520 nonbonded pdb=" NH2 ARG A 186 " pdb=" OE2 GLU H 204 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR N 159 " pdb=" OE2 GLU N 161 " model vdw 2.216 2.440 ... (remaining 151391 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.570 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 54.230 Find NCS groups from input model: 1.320 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: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 19460 Z= 0.316 Angle : 0.808 13.603 26369 Z= 0.466 Chirality : 0.047 0.317 3073 Planarity : 0.007 0.128 3451 Dihedral : 18.213 89.913 7273 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.46 % Favored : 97.42 % Rotamer: Outliers : 3.23 % Allowed : 31.46 % Favored : 65.31 % 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: 1.34 (0.17), residues: 2478 helix: 1.73 (0.15), residues: 1337 sheet: 1.73 (0.34), residues: 217 loop : -0.57 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP A 189 HIS 0.006 0.001 HIS D 138 PHE 0.023 0.002 PHE A 128 TYR 0.021 0.001 TYR C 98 ARG 0.012 0.001 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 762 time to evaluate : 2.175 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: C 179 GLN cc_start: 0.8976 (tp40) cc_final: 0.8357 (tp-100) REVERT: C 182 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7887 (ttp80) REVERT: H 85 GLU cc_start: 0.7597 (tp30) cc_final: 0.7379 (tp30) REVERT: H 202 ASP cc_start: 0.8425 (m-30) cc_final: 0.8213 (m-30) REVERT: I 126 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8669 (ptp) REVERT: J 152 ARG cc_start: 0.6289 (ptm160) cc_final: 0.5551 (ptm160) REVERT: K 104 PHE cc_start: 0.4428 (OUTLIER) cc_final: 0.3445 (m-80) REVERT: L 78 MET cc_start: 0.7914 (ptt) cc_final: 0.7707 (ptt) REVERT: M 91 ARG cc_start: 0.8919 (mtp85) cc_final: 0.8678 (mtp180) REVERT: M 152 ARG cc_start: 0.6330 (ptm160) cc_final: 0.5035 (ptm160) REVERT: N 117 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8614 (m) outliers start: 66 outliers final: 35 residues processed: 795 average time/residue: 1.3616 time to fit residues: 1209.6873 Evaluate side-chains 791 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 753 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 168 SER Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 216 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 141 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 122 GLN Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Chi-restraints excluded: chain N residue 225 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 222 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 58 ASN B 80 ASN C 58 ASN D 58 ASN E 132 ASN F 35 GLN F 171 GLN F 179 GLN G 38 ASN G 58 ASN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN J 98 ASN K 75 ASN K 98 ASN K 122 GLN K 175 ASN L 75 ASN M 75 ASN N 75 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19460 Z= 0.198 Angle : 0.570 9.472 26369 Z= 0.294 Chirality : 0.042 0.152 3073 Planarity : 0.005 0.065 3451 Dihedral : 6.025 77.012 2767 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.82 % Allowed : 25.64 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2478 helix: 2.17 (0.15), residues: 1358 sheet: 1.81 (0.33), residues: 217 loop : -0.58 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 189 HIS 0.005 0.001 HIS D 138 PHE 0.008 0.001 PHE I 58 TYR 0.012 0.001 TYR I 159 ARG 0.006 0.000 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 744 time to evaluate : 2.207 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: A 44 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6911 (tpt-90) REVERT: B 97 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: C 97 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8615 (mp10) REVERT: H 59 GLU cc_start: 0.8217 (mp0) cc_final: 0.7955 (mp0) REVERT: H 85 GLU cc_start: 0.7583 (tp30) cc_final: 0.7321 (tp30) REVERT: H 91 ARG cc_start: 0.8978 (mtp180) cc_final: 0.8775 (mtp180) REVERT: I 181 ARG cc_start: 0.8551 (ttt90) cc_final: 0.8128 (ttt180) REVERT: J 104 PHE cc_start: 0.4427 (OUTLIER) cc_final: 0.4101 (m-80) REVERT: J 152 ARG cc_start: 0.6312 (ptm160) cc_final: 0.5580 (ptm160) REVERT: K 104 PHE cc_start: 0.4181 (OUTLIER) cc_final: 0.3314 (m-80) REVERT: K 180 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7203 (mtp) REVERT: K 200 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7086 (ttp-110) REVERT: L 59 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8306 (mm-30) REVERT: L 122 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: L 181 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8308 (ttm-80) REVERT: M 60 GLU cc_start: 0.7662 (mp0) cc_final: 0.7352 (mp0) REVERT: M 146 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8165 (mpt) REVERT: M 152 ARG cc_start: 0.6341 (ptm160) cc_final: 0.4932 (ptm160) REVERT: M 179 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8110 (tmm-80) outliers start: 119 outliers final: 51 residues processed: 799 average time/residue: 1.3226 time to fit residues: 1182.6944 Evaluate side-chains 796 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 733 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 58 PHE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 179 ARG Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 222 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 80 ASN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 138 HIS C 139 GLN C 179 GLN D 58 ASN D 139 GLN E 58 ASN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 132 ASN G 171 GLN I 75 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN K 98 ASN K 115 GLN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN L 75 ASN L 175 ASN M 75 ASN M 98 ASN N 75 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 19460 Z= 0.403 Angle : 0.664 11.171 26369 Z= 0.344 Chirality : 0.045 0.176 3073 Planarity : 0.005 0.054 3451 Dihedral : 5.443 55.493 2725 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 6.02 % Allowed : 25.44 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.17), residues: 2478 helix: 1.93 (0.14), residues: 1365 sheet: 1.64 (0.33), residues: 217 loop : -0.63 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 189 HIS 0.006 0.001 HIS A 138 PHE 0.021 0.002 PHE I 104 TYR 0.018 0.002 TYR I 54 ARG 0.008 0.001 ARG H 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 765 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7218 (tpt-90) REVERT: A 97 GLN cc_start: 0.9113 (tp40) cc_final: 0.8872 (mm-40) REVERT: A 134 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: A 189 TRP cc_start: 0.8259 (m100) cc_final: 0.7841 (m100) REVERT: B 97 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8593 (mp10) REVERT: C 97 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: D 35 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: E 211 MET cc_start: 0.6616 (mtp) cc_final: 0.6390 (mtp) REVERT: G 53 ASP cc_start: 0.8192 (p0) cc_final: 0.7987 (p0) REVERT: H 59 GLU cc_start: 0.8339 (mp0) cc_final: 0.8010 (mp0) REVERT: H 85 GLU cc_start: 0.7738 (tp30) cc_final: 0.7402 (tp30) REVERT: H 87 MET cc_start: 0.6705 (mpt) cc_final: 0.6252 (mpt) REVERT: H 124 VAL cc_start: 0.8947 (m) cc_final: 0.8722 (t) REVERT: H 208 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6751 (mt) REVERT: I 104 PHE cc_start: 0.4231 (OUTLIER) cc_final: 0.3267 (m-80) REVERT: J 104 PHE cc_start: 0.4600 (OUTLIER) cc_final: 0.3800 (m-80) REVERT: J 146 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7574 (mpt) REVERT: K 104 PHE cc_start: 0.4489 (OUTLIER) cc_final: 0.3680 (m-80) REVERT: K 185 GLU cc_start: 0.7537 (tt0) cc_final: 0.6966 (tt0) REVERT: L 59 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: L 60 GLU cc_start: 0.7811 (mp0) cc_final: 0.7214 (mp0) REVERT: L 122 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: L 160 SER cc_start: 0.8789 (t) cc_final: 0.8565 (p) REVERT: L 181 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8294 (ttm-80) REVERT: N 59 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7992 (mp0) outliers start: 123 outliers final: 62 residues processed: 825 average time/residue: 1.3104 time to fit residues: 1210.7632 Evaluate side-chains 818 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 742 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 58 PHE Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 222 GLN Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 212 optimal weight: 0.0670 chunk 63 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 139 GLN A 171 GLN A 179 GLN B 58 ASN B 179 GLN C 179 GLN D 58 ASN E 58 ASN E 63 GLN E 80 ASN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 58 ASN G 138 HIS H 157 GLN I 75 ASN K 68 GLN K 75 ASN K 122 GLN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 ASN N 75 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19460 Z= 0.159 Angle : 0.559 10.124 26369 Z= 0.282 Chirality : 0.041 0.164 3073 Planarity : 0.005 0.042 3451 Dihedral : 4.836 49.484 2720 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.84 % Allowed : 27.01 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2478 helix: 2.33 (0.15), residues: 1358 sheet: 1.60 (0.33), residues: 217 loop : -0.56 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 189 HIS 0.003 0.001 HIS D 138 PHE 0.011 0.001 PHE I 104 TYR 0.013 0.001 TYR C 98 ARG 0.006 0.000 ARG M 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 731 time to evaluate : 2.368 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: C 97 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8637 (mp10) REVERT: C 134 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: E 189 TRP cc_start: 0.8308 (m100) cc_final: 0.7939 (m100) REVERT: E 211 MET cc_start: 0.6657 (mtp) cc_final: 0.6359 (mtp) REVERT: G 134 GLU cc_start: 0.8000 (pt0) cc_final: 0.7760 (pt0) REVERT: G 189 TRP cc_start: 0.8459 (m100) cc_final: 0.7865 (m100) REVERT: H 59 GLU cc_start: 0.8247 (mp0) cc_final: 0.7965 (mp0) REVERT: H 87 MET cc_start: 0.6519 (mpt) cc_final: 0.6079 (mpt) REVERT: H 104 PHE cc_start: 0.4268 (OUTLIER) cc_final: 0.3243 (m-80) REVERT: H 179 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7891 (tmm-80) REVERT: I 104 PHE cc_start: 0.4173 (OUTLIER) cc_final: 0.3453 (m-80) REVERT: J 104 PHE cc_start: 0.4567 (OUTLIER) cc_final: 0.4181 (m-80) REVERT: K 104 PHE cc_start: 0.4108 (OUTLIER) cc_final: 0.3523 (m-80) REVERT: L 59 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: L 60 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: L 87 MET cc_start: 0.5944 (mpt) cc_final: 0.5515 (mpt) REVERT: L 222 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8527 (tp-100) REVERT: M 60 GLU cc_start: 0.7773 (mp0) cc_final: 0.7456 (mp0) REVERT: N 59 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: N 164 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.5108 (ttm110) outliers start: 99 outliers final: 52 residues processed: 775 average time/residue: 1.3668 time to fit residues: 1182.4960 Evaluate side-chains 786 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 723 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 58 PHE Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 163 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 212 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 58 ASN C 138 HIS C 179 GLN D 58 ASN D 179 GLN E 58 ASN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 138 HIS G 179 GLN H 157 GLN I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 156 HIS M 75 ASN N 75 ASN N 115 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19460 Z= 0.238 Angle : 0.585 10.665 26369 Z= 0.299 Chirality : 0.042 0.166 3073 Planarity : 0.005 0.040 3451 Dihedral : 4.822 53.703 2719 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.63 % Allowed : 26.71 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2478 helix: 2.31 (0.15), residues: 1365 sheet: 1.54 (0.33), residues: 217 loop : -0.50 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 189 HIS 0.004 0.001 HIS D 138 PHE 0.015 0.002 PHE N 104 TYR 0.013 0.001 TYR C 98 ARG 0.007 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 729 time to evaluate : 2.052 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: A 44 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7246 (tpt-90) REVERT: B 97 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8511 (mp10) REVERT: B 211 MET cc_start: 0.6674 (mtp) cc_final: 0.6322 (mtt) REVERT: C 97 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8660 (mp10) REVERT: D 35 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6615 (mp10) REVERT: G 134 GLU cc_start: 0.8255 (pt0) cc_final: 0.7818 (pt0) REVERT: G 189 TRP cc_start: 0.8474 (m100) cc_final: 0.7764 (m100) REVERT: H 59 GLU cc_start: 0.8268 (mp0) cc_final: 0.7972 (mp0) REVERT: H 87 MET cc_start: 0.6684 (mpt) cc_final: 0.6204 (mpt) REVERT: H 104 PHE cc_start: 0.4345 (OUTLIER) cc_final: 0.3782 (m-80) REVERT: H 179 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7894 (tmm-80) REVERT: I 104 PHE cc_start: 0.4402 (OUTLIER) cc_final: 0.3453 (m-80) REVERT: I 146 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.6718 (mmt) REVERT: I 208 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6884 (mt) REVERT: J 104 PHE cc_start: 0.4498 (OUTLIER) cc_final: 0.3926 (m-80) REVERT: K 104 PHE cc_start: 0.4384 (OUTLIER) cc_final: 0.3698 (m-80) REVERT: K 146 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7020 (mpt) REVERT: L 59 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: L 60 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: L 87 MET cc_start: 0.6168 (mpt) cc_final: 0.5725 (mpt) REVERT: L 128 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: M 104 PHE cc_start: 0.4329 (OUTLIER) cc_final: 0.2992 (m-80) REVERT: N 59 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: N 104 PHE cc_start: 0.4413 (OUTLIER) cc_final: 0.4031 (m-80) outliers start: 115 outliers final: 63 residues processed: 777 average time/residue: 1.3670 time to fit residues: 1185.1173 Evaluate side-chains 808 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 727 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 103 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 104 PHE Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 58 ASN B 179 GLN C 58 ASN C 80 ASN C 179 GLN D 58 ASN D 179 GLN E 58 ASN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 50 GLN G 138 HIS G 179 GLN H 75 ASN I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 98 ASN L 156 HIS M 75 ASN N 75 ASN N 115 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19460 Z= 0.229 Angle : 0.594 10.726 26369 Z= 0.300 Chirality : 0.042 0.160 3073 Planarity : 0.005 0.041 3451 Dihedral : 4.794 53.290 2719 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.82 % Allowed : 27.25 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.18), residues: 2478 helix: 2.30 (0.15), residues: 1365 sheet: 1.47 (0.33), residues: 217 loop : -0.49 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 189 HIS 0.004 0.001 HIS D 138 PHE 0.014 0.001 PHE N 104 TYR 0.013 0.001 TYR C 98 ARG 0.007 0.000 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 730 time to evaluate : 2.248 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: A 44 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7227 (tpt-90) REVERT: B 97 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8526 (mp10) REVERT: B 134 GLU cc_start: 0.8365 (pt0) cc_final: 0.7502 (pt0) REVERT: B 189 TRP cc_start: 0.8318 (m100) cc_final: 0.8016 (m100) REVERT: B 211 MET cc_start: 0.6652 (mtp) cc_final: 0.6367 (mtt) REVERT: C 97 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8662 (mp10) REVERT: G 134 GLU cc_start: 0.8266 (pt0) cc_final: 0.7766 (pt0) REVERT: G 189 TRP cc_start: 0.8464 (m100) cc_final: 0.7694 (m100) REVERT: H 59 GLU cc_start: 0.8266 (mp0) cc_final: 0.7972 (mp0) REVERT: H 87 MET cc_start: 0.6700 (mpt) cc_final: 0.6218 (mpt) REVERT: H 104 PHE cc_start: 0.4343 (OUTLIER) cc_final: 0.3806 (m-80) REVERT: H 179 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7900 (tmm-80) REVERT: I 104 PHE cc_start: 0.4387 (OUTLIER) cc_final: 0.3423 (m-80) REVERT: I 146 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.6719 (mmt) REVERT: J 104 PHE cc_start: 0.4595 (OUTLIER) cc_final: 0.4002 (m-80) REVERT: K 104 PHE cc_start: 0.4471 (OUTLIER) cc_final: 0.3764 (m-80) REVERT: K 146 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7004 (mpt) REVERT: L 59 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: L 60 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: L 128 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: L 181 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8287 (ttm-80) REVERT: M 60 GLU cc_start: 0.7822 (mp0) cc_final: 0.7494 (mp0) REVERT: M 104 PHE cc_start: 0.4333 (OUTLIER) cc_final: 0.3032 (m-80) REVERT: M 146 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8243 (mpt) REVERT: N 59 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7925 (mp0) outliers start: 119 outliers final: 66 residues processed: 780 average time/residue: 1.3415 time to fit residues: 1170.1785 Evaluate side-chains 815 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 732 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 58 ASN C 80 ASN C 138 HIS C 179 GLN D 58 ASN D 179 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 132 ASN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 138 HIS G 171 GLN G 179 GLN H 98 ASN I 75 ASN K 75 ASN K 98 ASN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 ASN N 75 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19460 Z= 0.428 Angle : 0.698 11.769 26369 Z= 0.359 Chirality : 0.047 0.198 3073 Planarity : 0.005 0.045 3451 Dihedral : 5.102 56.367 2716 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.21 % Allowed : 26.86 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.17), residues: 2478 helix: 1.94 (0.14), residues: 1365 sheet: 1.32 (0.33), residues: 217 loop : -0.65 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 189 HIS 0.006 0.002 HIS A 138 PHE 0.023 0.002 PHE N 104 TYR 0.016 0.002 TYR I 54 ARG 0.010 0.001 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 761 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7019 (tpt-90) REVERT: A 134 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.6899 (pp20) REVERT: A 189 TRP cc_start: 0.8266 (m100) cc_final: 0.7964 (m100) REVERT: B 97 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.8640 (mp10) REVERT: B 189 TRP cc_start: 0.8336 (m100) cc_final: 0.7946 (m100) REVERT: B 211 MET cc_start: 0.6740 (mtp) cc_final: 0.6398 (mtt) REVERT: C 97 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.9040 (mm-40) REVERT: D 39 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7284 (mpt-90) REVERT: D 205 MET cc_start: 0.8367 (pmm) cc_final: 0.8106 (pmm) REVERT: E 134 GLU cc_start: 0.8414 (pt0) cc_final: 0.7893 (pt0) REVERT: F 134 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: H 59 GLU cc_start: 0.8362 (mp0) cc_final: 0.8021 (mp0) REVERT: H 60 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: H 87 MET cc_start: 0.6867 (mpt) cc_final: 0.6370 (mpt) REVERT: H 104 PHE cc_start: 0.4344 (OUTLIER) cc_final: 0.3226 (m-80) REVERT: H 146 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.6278 (mpt) REVERT: H 179 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7863 (tmm-80) REVERT: H 208 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6501 (mt) REVERT: I 104 PHE cc_start: 0.4262 (OUTLIER) cc_final: 0.3272 (m-80) REVERT: I 146 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.6637 (mmt) REVERT: I 208 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6997 (mt) REVERT: J 104 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.3765 (m-80) REVERT: J 146 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7702 (mpt) REVERT: K 104 PHE cc_start: 0.4342 (OUTLIER) cc_final: 0.3298 (m-80) REVERT: K 146 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7149 (mpt) REVERT: L 59 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: L 60 GLU cc_start: 0.7794 (mp0) cc_final: 0.7365 (mp0) REVERT: L 181 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8295 (ttm-80) REVERT: L 222 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8474 (tp-100) REVERT: M 104 PHE cc_start: 0.4306 (OUTLIER) cc_final: 0.3061 (m-80) REVERT: N 59 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7963 (mp0) outliers start: 127 outliers final: 69 residues processed: 811 average time/residue: 1.3205 time to fit residues: 1199.1189 Evaluate side-chains 836 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 746 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 181 ARG Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 128 GLN Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 139 GLN A 171 GLN A 179 GLN B 139 GLN B 179 GLN C 58 ASN C 80 ASN C 179 GLN D 58 ASN D 179 GLN E 138 HIS F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 58 ASN G 80 ASN G 138 HIS G 179 GLN H 157 GLN I 75 ASN K 75 ASN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN M 75 ASN N 75 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19460 Z= 0.263 Angle : 0.654 12.516 26369 Z= 0.328 Chirality : 0.044 0.163 3073 Planarity : 0.005 0.042 3451 Dihedral : 4.860 55.504 2714 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 5.33 % Allowed : 28.33 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.17), residues: 2478 helix: 2.10 (0.14), residues: 1365 sheet: 1.34 (0.33), residues: 217 loop : -0.60 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 189 HIS 0.004 0.001 HIS D 138 PHE 0.015 0.002 PHE H 104 TYR 0.015 0.001 TYR D 98 ARG 0.007 0.000 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 744 time to evaluate : 2.121 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 44 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7294 (tpt-90) REVERT: B 97 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: C 97 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: D 205 MET cc_start: 0.8321 (pmm) cc_final: 0.8097 (pmm) REVERT: G 134 GLU cc_start: 0.8310 (pt0) cc_final: 0.7409 (pt0) REVERT: G 179 GLN cc_start: 0.8954 (tp40) cc_final: 0.8530 (tp-100) REVERT: G 182 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8210 (ttp80) REVERT: G 189 TRP cc_start: 0.8453 (m100) cc_final: 0.7745 (m100) REVERT: H 59 GLU cc_start: 0.8288 (mp0) cc_final: 0.7991 (mp0) REVERT: H 87 MET cc_start: 0.6734 (mpt) cc_final: 0.6265 (mpt) REVERT: H 104 PHE cc_start: 0.4444 (OUTLIER) cc_final: 0.3860 (m-80) REVERT: H 179 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7862 (tmm-80) REVERT: I 104 PHE cc_start: 0.4483 (OUTLIER) cc_final: 0.3661 (m-80) REVERT: I 146 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.6651 (mmt) REVERT: J 104 PHE cc_start: 0.4541 (OUTLIER) cc_final: 0.3796 (m-80) REVERT: J 146 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7587 (mpt) REVERT: J 181 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7952 (ttm-80) REVERT: K 104 PHE cc_start: 0.4407 (OUTLIER) cc_final: 0.3535 (m-80) REVERT: K 126 MET cc_start: 0.8822 (ppp) cc_final: 0.8615 (ppp) REVERT: K 146 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7109 (mpt) REVERT: L 59 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: L 60 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: L 128 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8157 (pt0) REVERT: M 104 PHE cc_start: 0.4238 (OUTLIER) cc_final: 0.3369 (m-80) REVERT: N 59 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: N 164 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.5308 (ttm110) outliers start: 109 outliers final: 67 residues processed: 789 average time/residue: 1.3535 time to fit residues: 1193.8788 Evaluate side-chains 830 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 745 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 GLN Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 128 GLN Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 0.3980 chunk 226 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 208 optimal weight: 0.4980 chunk 219 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 GLN A 171 GLN A 179 GLN B 58 ASN B 171 GLN B 179 GLN C 58 ASN C 179 GLN D 58 ASN D 138 HIS D 179 GLN F 58 ASN F 171 GLN F 179 GLN G 50 GLN G 58 ASN G 138 HIS I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19460 Z= 0.210 Angle : 0.635 13.321 26369 Z= 0.317 Chirality : 0.043 0.177 3073 Planarity : 0.005 0.039 3451 Dihedral : 4.721 56.697 2714 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.09 % Allowed : 28.67 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2478 helix: 2.22 (0.15), residues: 1365 sheet: 1.44 (0.33), residues: 217 loop : -0.53 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 189 HIS 0.005 0.001 HIS D 138 PHE 0.013 0.001 PHE H 104 TYR 0.016 0.001 TYR C 98 ARG 0.008 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 734 time to evaluate : 2.322 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: A 44 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7217 (tpt-90) REVERT: B 97 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8542 (mp10) REVERT: C 39 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7518 (mtt-85) REVERT: F 114 MET cc_start: 0.7685 (tpt) cc_final: 0.7367 (tpt) REVERT: F 134 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: F 189 TRP cc_start: 0.8222 (m100) cc_final: 0.7725 (m100) REVERT: G 134 GLU cc_start: 0.8295 (pt0) cc_final: 0.7615 (pt0) REVERT: G 182 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8217 (ttp80) REVERT: G 189 TRP cc_start: 0.8465 (m100) cc_final: 0.7835 (m100) REVERT: H 59 GLU cc_start: 0.8255 (mp0) cc_final: 0.7963 (mp0) REVERT: H 87 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6242 (mpt) REVERT: H 104 PHE cc_start: 0.4618 (OUTLIER) cc_final: 0.4268 (m-80) REVERT: H 179 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7883 (tmm-80) REVERT: I 78 MET cc_start: 0.7486 (ttm) cc_final: 0.7241 (ttp) REVERT: I 104 PHE cc_start: 0.4442 (OUTLIER) cc_final: 0.3654 (m-80) REVERT: I 146 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.6734 (mmt) REVERT: J 104 PHE cc_start: 0.4567 (OUTLIER) cc_final: 0.3900 (m-80) REVERT: K 104 PHE cc_start: 0.4267 (OUTLIER) cc_final: 0.3575 (m-80) REVERT: K 146 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.6978 (mpt) REVERT: L 59 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: L 60 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: L 222 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8445 (tp-100) REVERT: M 104 PHE cc_start: 0.4281 (OUTLIER) cc_final: 0.3590 (m-80) REVERT: M 146 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8207 (mpt) REVERT: N 59 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: N 164 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.5223 (ttm110) outliers start: 104 outliers final: 65 residues processed: 780 average time/residue: 1.3292 time to fit residues: 1160.2907 Evaluate side-chains 804 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 722 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 PHE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 0.8980 chunk 232 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 161 optimal weight: 0.0980 chunk 244 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 171 GLN A 179 GLN B 179 GLN C 58 ASN C 179 GLN D 58 ASN D 138 HIS D 179 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN F 171 GLN F 179 GLN G 50 GLN I 75 ASN K 75 ASN K 98 ASN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19460 Z= 0.183 Angle : 0.658 13.313 26369 Z= 0.321 Chirality : 0.042 0.185 3073 Planarity : 0.004 0.042 3451 Dihedral : 4.586 57.251 2711 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.01 % Allowed : 29.99 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.18), residues: 2478 helix: 2.28 (0.14), residues: 1358 sheet: 1.79 (0.33), residues: 210 loop : -0.46 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 189 HIS 0.007 0.001 HIS D 138 PHE 0.012 0.001 PHE I 104 TYR 0.019 0.001 TYR D 98 ARG 0.009 0.000 ARG N 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 724 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.8408 (pt0) cc_final: 0.7192 (pt0) REVERT: C 39 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7497 (mtt-85) REVERT: E 134 GLU cc_start: 0.8189 (pt0) cc_final: 0.7076 (pt0) REVERT: E 189 TRP cc_start: 0.8159 (m100) cc_final: 0.7703 (m100) REVERT: G 134 GLU cc_start: 0.8284 (pt0) cc_final: 0.7583 (pt0) REVERT: G 179 GLN cc_start: 0.8905 (tp40) cc_final: 0.8493 (tp-100) REVERT: G 189 TRP cc_start: 0.8473 (m100) cc_final: 0.7788 (m100) REVERT: G 206 THR cc_start: 0.8099 (m) cc_final: 0.7812 (p) REVERT: H 59 GLU cc_start: 0.8245 (mp0) cc_final: 0.7951 (mp0) REVERT: H 87 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6184 (mpt) REVERT: I 104 PHE cc_start: 0.4395 (OUTLIER) cc_final: 0.3647 (m-80) REVERT: J 104 PHE cc_start: 0.4576 (OUTLIER) cc_final: 0.4027 (m-80) REVERT: K 104 PHE cc_start: 0.4005 (OUTLIER) cc_final: 0.3397 (m-80) REVERT: K 146 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.6930 (mpt) REVERT: K 208 ILE cc_start: 0.7030 (mt) cc_final: 0.6618 (mt) REVERT: L 59 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: L 60 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: L 78 MET cc_start: 0.7930 (ptt) cc_final: 0.7716 (ptt) REVERT: L 222 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8402 (tp-100) REVERT: M 104 PHE cc_start: 0.4217 (OUTLIER) cc_final: 0.3675 (m-80) REVERT: M 146 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8171 (mpt) REVERT: N 59 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: N 164 ARG cc_start: 0.5548 (OUTLIER) cc_final: 0.5160 (ttm110) REVERT: N 200 ARG cc_start: 0.7015 (mtm110) cc_final: 0.6741 (mtm110) outliers start: 82 outliers final: 52 residues processed: 756 average time/residue: 1.3408 time to fit residues: 1133.7360 Evaluate side-chains 781 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 718 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 83 CYS Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 83 CYS Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 SER Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 146 MET Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 223 VAL Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 216 SER Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain N residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 171 GLN A 179 GLN B 38 ASN B 171 GLN B 179 GLN C 58 ASN C 179 GLN D 58 ASN D 138 HIS E 58 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN E 179 GLN F 58 ASN F 138 HIS F 171 GLN F 179 GLN G 138 HIS G 171 GLN ** H 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105140 restraints weight = 28352.593| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.75 r_work: 0.3517 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19460 Z= 0.203 Angle : 0.679 13.576 26369 Z= 0.330 Chirality : 0.042 0.167 3073 Planarity : 0.005 0.042 3451 Dihedral : 4.661 58.050 2711 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.77 % Allowed : 31.21 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.17), residues: 2478 helix: 2.24 (0.14), residues: 1365 sheet: 1.82 (0.33), residues: 210 loop : -0.37 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 189 HIS 0.020 0.001 HIS D 138 PHE 0.014 0.001 PHE B 190 TYR 0.019 0.001 TYR D 98 ARG 0.010 0.001 ARG N 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14138.99 seconds wall clock time: 250 minutes 12.98 seconds (15012.98 seconds total)