Starting phenix.real_space_refine on Wed Aug 7 04:38:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/08_2024/8xn4_38497.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/08_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_38497/08_2024/8xn4_38497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/08_2024/8xn4_38497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/08_2024/8xn4_38497.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn4_38497/08_2024/8xn4_38497.cif" } 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-5409/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: 10.57, 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: 7.68 Conformation dependent library (CDL) restraints added in 3.5 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: 2.72 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: 7.85 Time building geometry restraints manager: 8.42 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 3.120 nonbonded pdb=" OD2 ASP I 202 " pdb=" OH TYR I 217 " model vdw 2.205 3.040 nonbonded pdb=" O GLU L 171 " pdb=" ND2 ASN L 175 " model vdw 2.211 3.120 nonbonded pdb=" NH2 ARG A 186 " pdb=" OE2 GLU H 204 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR N 159 " pdb=" OE2 GLU N 161 " model vdw 2.216 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 54.570 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.000 ------------------------------------------------------------------------------- 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 : 2.094 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: 1.2199 time to fit residues: 1086.2822 Evaluate side-chains 791 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 753 time to evaluate : 2.078 ------------------------------------------------------------------------------- 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: 0.8980 chunk 185 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 192 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 E 138 HIS E 139 GLN F 35 GLN F 171 GLN F 179 GLN G 38 ASN G 58 ASN G 116 GLN H 75 ASN H 157 GLN I 75 ASN J 98 ASN K 75 ASN K 98 ASN K 122 GLN K 175 ASN L 75 ASN L 156 HIS M 75 ASN N 75 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19460 Z= 0.185 Angle : 0.583 9.306 26369 Z= 0.301 Chirality : 0.042 0.150 3073 Planarity : 0.005 0.065 3451 Dihedral : 6.164 77.319 2767 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.43 % Allowed : 25.44 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.17), residues: 2478 helix: 2.19 (0.15), residues: 1358 sheet: 1.80 (0.33), residues: 217 loop : -0.54 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.001 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 862 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 751 time to evaluate : 2.123 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: 0.7795 (OUTLIER) cc_final: 0.7538 (tpt-90) REVERT: B 97 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8361 (mp10) REVERT: H 59 GLU cc_start: 0.8203 (mp0) cc_final: 0.7936 (mp0) REVERT: H 85 GLU cc_start: 0.7547 (tp30) cc_final: 0.7320 (tp30) REVERT: J 152 ARG cc_start: 0.6305 (ptm160) cc_final: 0.5602 (ptm160) REVERT: K 104 PHE cc_start: 0.4093 (OUTLIER) cc_final: 0.3184 (m-80) REVERT: K 180 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7191 (mtp) REVERT: L 59 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: L 60 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: L 122 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: M 60 GLU cc_start: 0.7637 (mp0) cc_final: 0.7344 (mp0) REVERT: M 91 ARG cc_start: 0.8911 (mtp85) cc_final: 0.8705 (mtp180) REVERT: M 146 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8067 (mpt) REVERT: M 152 ARG cc_start: 0.6338 (ptm160) cc_final: 0.4956 (ptm160) REVERT: M 179 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8122 (tmm-80) outliers start: 111 outliers final: 43 residues processed: 801 average time/residue: 1.2379 time to fit residues: 1114.4283 Evaluate side-chains 790 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 738 time to evaluate : 2.125 ------------------------------------------------------------------------------- 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 D residue 43 GLU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 116 GLN Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 128 GLN Chi-restraints excluded: chain J residue 160 SER 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 107 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 177 ILE 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 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 122 GLN 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 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 208 ILE 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: 7.9990 chunk 69 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 240 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 178 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 38 ASN B 58 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 179 GLN C 58 ASN C 138 HIS C 139 GLN C 179 GLN D 58 ASN D 139 GLN 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 58 ASN G 132 ASN G 171 GLN I 75 ASN K 75 ASN K 98 ASN K 115 GLN K 222 GLN L 75 ASN L 175 ASN M 75 ASN M 98 ASN N 75 ASN N 115 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19460 Z= 0.375 Angle : 0.657 10.880 26369 Z= 0.341 Chirality : 0.045 0.167 3073 Planarity : 0.005 0.052 3451 Dihedral : 5.621 56.194 2728 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.68 % Allowed : 25.05 % Favored : 69.28 % 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: 1.59 (0.17), residues: 2478 helix: 2.00 (0.14), residues: 1365 sheet: 1.55 (0.33), residues: 217 loop : -0.56 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 189 HIS 0.006 0.001 HIS A 138 PHE 0.018 0.002 PHE N 104 TYR 0.017 0.002 TYR I 54 ARG 0.010 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 874 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 758 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7235 (tpt-90) REVERT: A 74 ASP cc_start: 0.8437 (m-30) cc_final: 0.8002 (m-30) REVERT: A 97 GLN cc_start: 0.9075 (tp40) cc_final: 0.8822 (mm-40) REVERT: A 134 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7163 (pp20) REVERT: A 189 TRP cc_start: 0.8243 (m100) cc_final: 0.7888 (m100) REVERT: B 97 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8498 (mp10) REVERT: C 97 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8652 (mp10) REVERT: D 35 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6759 (mp10) REVERT: D 179 GLN cc_start: 0.9099 (tp40) cc_final: 0.8865 (mm-40) REVERT: H 59 GLU cc_start: 0.8315 (mp0) cc_final: 0.8012 (mp0) REVERT: H 85 GLU cc_start: 0.7735 (tp30) cc_final: 0.7418 (tp30) REVERT: H 87 MET cc_start: 0.6748 (mpt) cc_final: 0.6287 (mpt) REVERT: H 146 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.6362 (mpt) REVERT: I 104 PHE cc_start: 0.4286 (OUTLIER) cc_final: 0.3488 (m-80) REVERT: J 61 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7906 (mtp-110) REVERT: J 104 PHE cc_start: 0.4579 (OUTLIER) cc_final: 0.4012 (m-80) REVERT: J 146 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7505 (mpt) REVERT: J 204 GLU cc_start: 0.8255 (tp30) cc_final: 0.8017 (tp30) REVERT: K 104 PHE cc_start: 0.4487 (OUTLIER) cc_final: 0.3760 (m-80) REVERT: K 185 GLU cc_start: 0.7538 (tt0) cc_final: 0.6996 (tt0) REVERT: L 59 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: L 60 GLU cc_start: 0.7828 (mp0) cc_final: 0.7166 (mp0) REVERT: N 59 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: N 181 ARG cc_start: 0.8644 (tmm-80) cc_final: 0.8422 (ttt180) outliers start: 116 outliers final: 55 residues processed: 813 average time/residue: 1.2641 time to fit residues: 1152.7835 Evaluate side-chains 832 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 764 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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 101 ASN 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 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 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 203 ASP Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 108 THR 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 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 61 ARG Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 146 MET Chi-restraints excluded: chain J residue 160 SER 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 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 128 GLN Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 161 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 216 SER 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 141 THR 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 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 38 ASN B 58 ASN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 179 GLN C 138 HIS C 179 GLN D 58 ASN E 58 ASN 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 H 157 GLN I 75 ASN K 68 GLN K 75 ASN L 75 ASN ** L 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 ASN N 75 ASN N 115 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19460 Z= 0.250 Angle : 0.614 11.687 26369 Z= 0.313 Chirality : 0.043 0.161 3073 Planarity : 0.005 0.044 3451 Dihedral : 5.167 49.343 2722 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.43 % Allowed : 26.27 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.17), residues: 2478 helix: 2.19 (0.15), residues: 1358 sheet: 1.45 (0.34), residues: 217 loop : -0.59 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 189 HIS 0.003 0.001 HIS A 138 PHE 0.014 0.001 PHE I 104 TYR 0.011 0.001 TYR K 159 ARG 0.011 0.001 ARG H 152 *********************** 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 866 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 755 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7595 (tpt-90) REVERT: A 97 GLN cc_start: 0.9050 (tp40) cc_final: 0.8775 (mm-40) REVERT: A 134 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: A 189 TRP cc_start: 0.8221 (m100) cc_final: 0.7969 (m100) REVERT: C 97 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8665 (mp10) REVERT: D 179 GLN cc_start: 0.9064 (tp40) cc_final: 0.8837 (mm-40) REVERT: G 134 GLU cc_start: 0.8340 (pt0) cc_final: 0.7920 (pt0) REVERT: G 189 TRP cc_start: 0.8367 (m100) cc_final: 0.7944 (m100) REVERT: H 59 GLU cc_start: 0.8276 (mp0) cc_final: 0.7978 (mp0) REVERT: H 87 MET cc_start: 0.6706 (mpt) cc_final: 0.6224 (mpt) REVERT: H 104 PHE cc_start: 0.4251 (OUTLIER) cc_final: 0.3151 (m-80) REVERT: H 146 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.6344 (mpt) REVERT: H 208 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6899 (mt) REVERT: I 104 PHE cc_start: 0.4270 (OUTLIER) cc_final: 0.3418 (m-80) REVERT: J 61 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7831 (mtp180) REVERT: J 104 PHE cc_start: 0.4743 (OUTLIER) cc_final: 0.4332 (m-80) REVERT: J 146 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7291 (mpt) REVERT: J 202 ASP cc_start: 0.8627 (m-30) cc_final: 0.8308 (m-30) REVERT: K 104 PHE cc_start: 0.4281 (OUTLIER) cc_final: 0.3631 (m-80) REVERT: L 59 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: L 60 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: L 87 MET cc_start: 0.6094 (mpt) cc_final: 0.5650 (mpt) REVERT: M 60 GLU cc_start: 0.7803 (mp0) cc_final: 0.7464 (mp0) REVERT: M 91 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8670 (mtp180) REVERT: N 59 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: N 164 ARG cc_start: 0.5750 (OUTLIER) cc_final: 0.5311 (ttm110) REVERT: N 202 ASP cc_start: 0.8617 (m-30) cc_final: 0.8383 (m-30) outliers start: 111 outliers final: 62 residues processed: 805 average time/residue: 1.3338 time to fit residues: 1212.7219 Evaluate side-chains 814 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 737 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 85 SER 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 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 E residue 42 ASN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 134 GLU 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 50 GLN 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 146 MET Chi-restraints excluded: chain H residue 160 SER 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 185 GLU Chi-restraints excluded: chain J residue 61 ARG 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 126 MET Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 146 MET 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 124 VAL Chi-restraints excluded: chain K residue 180 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 161 GLU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain M residue 61 ARG 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 70 ASP Chi-restraints excluded: chain N residue 108 THR 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 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: 2.9990 chunk 134 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 179 GLN D 58 ASN E 58 ASN E 132 ASN F 58 ASN F 171 GLN F 179 GLN G 179 GLN 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 N 115 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19460 Z= 0.245 Angle : 0.614 10.207 26369 Z= 0.314 Chirality : 0.043 0.156 3073 Planarity : 0.005 0.040 3451 Dihedral : 4.957 50.466 2720 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.38 % Allowed : 26.08 % 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: 1.73 (0.17), residues: 2478 helix: 2.21 (0.14), residues: 1358 sheet: 1.30 (0.33), residues: 217 loop : -0.58 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 189 HIS 0.003 0.001 HIS D 138 PHE 0.015 0.001 PHE N 104 TYR 0.011 0.001 TYR I 116 ARG 0.007 0.001 ARG C 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 853 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 743 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7610 (tpt-90) REVERT: A 97 GLN cc_start: 0.9058 (tp40) cc_final: 0.8785 (mm-40) REVERT: B 97 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: B 108 MET cc_start: 0.8470 (ptp) cc_final: 0.8267 (ptm) REVERT: C 97 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8673 (mp10) REVERT: E 211 MET cc_start: 0.6981 (mtp) cc_final: 0.6733 (mtt) REVERT: G 134 GLU cc_start: 0.8357 (pt0) cc_final: 0.7937 (pt0) REVERT: G 189 TRP cc_start: 0.8380 (m100) cc_final: 0.7993 (m100) REVERT: H 59 GLU cc_start: 0.8274 (mp0) cc_final: 0.7976 (mp0) REVERT: H 87 MET cc_start: 0.6875 (mpt) cc_final: 0.6549 (mpt) REVERT: H 104 PHE cc_start: 0.4296 (OUTLIER) cc_final: 0.3155 (m-80) REVERT: H 146 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.6349 (mpt) REVERT: H 176 GLU cc_start: 0.8334 (tp30) cc_final: 0.8130 (tp30) REVERT: H 179 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7962 (tmm-80) REVERT: I 104 PHE cc_start: 0.4538 (OUTLIER) cc_final: 0.3593 (m-80) REVERT: J 61 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7823 (mtp-110) REVERT: J 104 PHE cc_start: 0.4610 (OUTLIER) cc_final: 0.4163 (m-80) REVERT: J 146 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7336 (mpt) REVERT: K 104 PHE cc_start: 0.4340 (OUTLIER) cc_final: 0.3642 (m-80) REVERT: K 204 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7903 (tm-30) REVERT: L 59 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: L 60 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: L 87 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5838 (mpt) REVERT: L 126 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8394 (ptt) REVERT: M 60 GLU cc_start: 0.7825 (mp0) cc_final: 0.7515 (mp0) REVERT: M 104 PHE cc_start: 0.4290 (OUTLIER) cc_final: 0.2976 (m-80) REVERT: N 59 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: N 104 PHE cc_start: 0.4395 (OUTLIER) cc_final: 0.3971 (m-80) REVERT: N 122 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7308 (tp40) REVERT: N 164 ARG cc_start: 0.5738 (OUTLIER) cc_final: 0.5310 (ttm110) REVERT: N 181 ARG cc_start: 0.8562 (tmm-80) cc_final: 0.8362 (ttt180) REVERT: N 202 ASP cc_start: 0.8600 (m-30) cc_final: 0.8313 (m-30) outliers start: 110 outliers final: 58 residues processed: 795 average time/residue: 1.2906 time to fit residues: 1148.0704 Evaluate side-chains 811 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 733 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 161 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 55 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain D residue 43 GLU 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 206 THR Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 134 GLU 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 203 ASP 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 117 VAL Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 227 ARG 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 I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 61 ARG 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 117 VAL Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 146 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 124 VAL 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 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 126 MET Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 152 ARG 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 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 122 GLN 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 223 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 237 optimal weight: 0.5980 chunk 196 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 58 ASN B 179 GLN C 138 HIS C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 63 GLN E 132 ASN F 58 ASN F 171 GLN F 179 GLN G 50 GLN G 179 GLN H 98 ASN ** H 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19460 Z= 0.209 Angle : 0.600 10.978 26369 Z= 0.303 Chirality : 0.042 0.151 3073 Planarity : 0.004 0.039 3451 Dihedral : 4.654 50.264 2714 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.72 % Allowed : 26.86 % Favored : 67.42 % 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: 1.85 (0.18), residues: 2478 helix: 2.32 (0.15), residues: 1358 sheet: 1.27 (0.34), residues: 217 loop : -0.52 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 189 HIS 0.003 0.001 HIS C 138 PHE 0.014 0.001 PHE N 104 TYR 0.010 0.001 TYR J 159 ARG 0.006 0.000 ARG M 91 *********************** 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 852 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 735 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7545 (tpt-90) REVERT: C 97 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8675 (mp10) REVERT: E 211 MET cc_start: 0.7046 (mtp) cc_final: 0.6826 (mtt) REVERT: G 134 GLU cc_start: 0.8387 (pt0) cc_final: 0.7991 (pt0) REVERT: G 189 TRP cc_start: 0.8388 (m100) cc_final: 0.8053 (m100) REVERT: H 59 GLU cc_start: 0.8251 (mp0) cc_final: 0.7954 (mp0) REVERT: H 87 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6550 (mpt) REVERT: H 104 PHE cc_start: 0.4296 (OUTLIER) cc_final: 0.3763 (m-80) REVERT: H 179 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7977 (tmm-80) REVERT: H 208 ILE cc_start: 0.6735 (mt) cc_final: 0.6459 (mt) REVERT: I 59 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: I 104 PHE cc_start: 0.4463 (OUTLIER) cc_final: 0.3497 (m-80) REVERT: J 104 PHE cc_start: 0.4673 (OUTLIER) cc_final: 0.4259 (m-80) REVERT: J 181 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8002 (ttm-80) REVERT: K 104 PHE cc_start: 0.4429 (OUTLIER) cc_final: 0.3755 (m-80) REVERT: K 204 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7878 (tm-30) REVERT: L 59 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: L 60 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: L 87 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5801 (mpt) REVERT: L 135 VAL cc_start: 0.7002 (t) cc_final: 0.6785 (p) REVERT: M 60 GLU cc_start: 0.7818 (mp0) cc_final: 0.7493 (mp0) REVERT: M 104 PHE cc_start: 0.4351 (OUTLIER) cc_final: 0.3022 (m-80) REVERT: N 59 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: N 104 PHE cc_start: 0.4464 (OUTLIER) cc_final: 0.4111 (m-80) REVERT: N 122 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7253 (tp40) REVERT: N 164 ARG cc_start: 0.5693 (OUTLIER) cc_final: 0.5271 (ttm110) REVERT: N 202 ASP cc_start: 0.8609 (m-30) cc_final: 0.8293 (m-30) outliers start: 117 outliers final: 64 residues processed: 785 average time/residue: 1.2592 time to fit residues: 1109.3487 Evaluate side-chains 804 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 722 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 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 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 120 SER 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 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 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 179 ARG Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU 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 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 117 VAL Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain J residue 223 VAL 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 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 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 208 ILE Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 78 MET 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 122 GLN 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 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: 0.9990 chunk 26 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 0.0470 chunk 109 optimal weight: 4.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- 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 58 ASN B 171 GLN B 179 GLN C 58 ASN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 58 ASN E 132 ASN F 35 GLN F 58 ASN F 171 GLN F 179 GLN G 50 GLN G 179 GLN H 157 GLN H 222 GLN 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: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19460 Z= 0.188 Angle : 0.606 13.304 26369 Z= 0.304 Chirality : 0.042 0.153 3073 Planarity : 0.004 0.039 3451 Dihedral : 4.545 50.022 2713 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.09 % Allowed : 27.59 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.18), residues: 2478 helix: 2.40 (0.15), residues: 1358 sheet: 1.52 (0.34), residues: 210 loop : -0.42 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 189 HIS 0.003 0.001 HIS D 138 PHE 0.012 0.001 PHE N 104 TYR 0.016 0.001 TYR E 98 ARG 0.007 0.000 ARG H 91 *********************** 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 832 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 728 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7485 (tpt-90) REVERT: B 97 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8398 (mp10) REVERT: C 97 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8662 (mp10) REVERT: D 205 MET cc_start: 0.8230 (pmm) cc_final: 0.8004 (pmm) REVERT: E 211 MET cc_start: 0.7093 (mtp) cc_final: 0.6866 (mtt) REVERT: G 134 GLU cc_start: 0.8362 (pt0) cc_final: 0.7850 (pt0) REVERT: G 189 TRP cc_start: 0.8391 (m100) cc_final: 0.7909 (m100) REVERT: H 59 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: H 87 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6538 (mpt) REVERT: H 104 PHE cc_start: 0.4488 (OUTLIER) cc_final: 0.4123 (m-80) REVERT: H 179 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7985 (tmm-80) REVERT: I 59 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: I 104 PHE cc_start: 0.4414 (OUTLIER) cc_final: 0.3488 (m-80) REVERT: J 104 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.4241 (m-80) REVERT: J 181 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7991 (ttm-80) REVERT: K 104 PHE cc_start: 0.4397 (OUTLIER) cc_final: 0.3692 (m-80) REVERT: K 204 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7869 (tm-30) REVERT: L 59 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: L 60 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: L 87 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5817 (mpt) REVERT: M 60 GLU cc_start: 0.7807 (mp0) cc_final: 0.7482 (mp0) REVERT: M 104 PHE cc_start: 0.4293 (OUTLIER) cc_final: 0.3541 (m-80) REVERT: M 179 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8050 (mmm-85) REVERT: N 59 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: N 122 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7256 (tp40) REVERT: N 164 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.5207 (ttm110) REVERT: N 202 ASP cc_start: 0.8591 (m-30) cc_final: 0.8262 (m-30) outliers start: 104 outliers final: 57 residues processed: 771 average time/residue: 1.2564 time to fit residues: 1087.3309 Evaluate side-chains 793 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 716 time to evaluate : 1.964 ------------------------------------------------------------------------------- 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 55 ASP Chi-restraints excluded: chain C residue 97 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 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 120 SER 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 G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 59 GLU 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 117 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU 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 181 ARG 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 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 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 220 ILE Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR 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 59 GLU Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 122 GLN 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 167 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 71 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 58 ASN B 171 GLN B 179 GLN C 58 ASN C 179 GLN D 58 ASN D 179 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 132 ASN F 58 ASN F 171 GLN F 179 GLN G 80 ASN G 171 GLN G 179 GLN H 98 ASN H 157 GLN 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19460 Z= 0.331 Angle : 0.684 12.546 26369 Z= 0.346 Chirality : 0.045 0.196 3073 Planarity : 0.005 0.041 3451 Dihedral : 4.840 51.315 2713 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.53 % Allowed : 27.59 % Favored : 66.88 % 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: 1.69 (0.17), residues: 2478 helix: 2.12 (0.14), residues: 1365 sheet: 1.19 (0.33), residues: 217 loop : -0.46 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 189 HIS 0.006 0.001 HIS D 138 PHE 0.020 0.002 PHE N 104 TYR 0.013 0.001 TYR E 198 ARG 0.008 0.001 ARG A 182 *********************** 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 854 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 741 time to evaluate : 2.110 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: 0.7958 (OUTLIER) cc_final: 0.7222 (tpt-90) REVERT: A 74 ASP cc_start: 0.8428 (m-30) cc_final: 0.8060 (m-30) REVERT: A 97 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: B 97 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: C 97 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8656 (mp10) REVERT: D 205 MET cc_start: 0.8354 (pmm) cc_final: 0.8101 (pmm) REVERT: D 211 MET cc_start: 0.7022 (ttp) cc_final: 0.6621 (ttm) REVERT: E 211 MET cc_start: 0.7022 (mtp) cc_final: 0.6740 (mtt) REVERT: G 206 THR cc_start: 0.8207 (m) cc_final: 0.7832 (p) REVERT: H 59 GLU cc_start: 0.8294 (mp0) cc_final: 0.7988 (mp0) REVERT: H 60 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: H 87 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6543 (mpt) REVERT: H 104 PHE cc_start: 0.4319 (OUTLIER) cc_final: 0.3564 (m-80) REVERT: H 176 GLU cc_start: 0.8364 (tp30) cc_final: 0.7962 (tp30) REVERT: H 179 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7969 (tmm-80) REVERT: H 208 ILE cc_start: 0.6768 (mt) cc_final: 0.5770 (mt) REVERT: I 59 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: I 104 PHE cc_start: 0.4531 (OUTLIER) cc_final: 0.3588 (m-80) REVERT: J 61 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7816 (mtp-110) REVERT: J 104 PHE cc_start: 0.4635 (OUTLIER) cc_final: 0.3948 (m-80) REVERT: K 104 PHE cc_start: 0.4232 (OUTLIER) cc_final: 0.3368 (m-80) REVERT: K 126 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8048 (ppp) REVERT: K 146 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7941 (mpt) REVERT: K 204 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7941 (tm-30) REVERT: L 59 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: L 60 GLU cc_start: 0.7761 (mp0) cc_final: 0.7299 (mp0) REVERT: L 87 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.5962 (mpt) REVERT: M 60 GLU cc_start: 0.7892 (mp0) cc_final: 0.7545 (mp0) REVERT: M 104 PHE cc_start: 0.4283 (OUTLIER) cc_final: 0.3331 (m-80) REVERT: M 179 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8038 (mmm-85) REVERT: N 59 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: N 85 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6335 (mt-10) REVERT: N 152 ARG cc_start: 0.7620 (ptt180) cc_final: 0.7414 (ptt180) REVERT: N 202 ASP cc_start: 0.8645 (m-30) cc_final: 0.8294 (m-30) outliers start: 113 outliers final: 65 residues processed: 786 average time/residue: 1.2615 time to fit residues: 1110.9150 Evaluate side-chains 828 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 743 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 97 GLN 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 170 SER Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 43 GLU 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 120 SER 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 170 SER Chi-restraints excluded: chain G residue 203 ASP 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 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 122 GLN Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU 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 I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 61 ARG Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 184 LEU 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 126 MET 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 103 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR 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 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 160 SER Chi-restraints excluded: chain N residue 162 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 208 optimal weight: 0.0980 chunk 219 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 179 GLN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 132 ASN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN F 171 GLN F 179 GLN G 38 ASN G 80 ASN G 179 GLN H 75 ASN I 75 ASN K 75 ASN L 75 ASN L 156 HIS M 75 ASN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19460 Z= 0.183 Angle : 0.634 13.127 26369 Z= 0.316 Chirality : 0.042 0.154 3073 Planarity : 0.004 0.038 3451 Dihedral : 4.585 49.297 2711 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.91 % Allowed : 29.60 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 2478 helix: 2.31 (0.15), residues: 1358 sheet: 1.50 (0.34), residues: 210 loop : -0.38 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 189 HIS 0.004 0.001 HIS D 138 PHE 0.010 0.001 PHE H 104 TYR 0.017 0.001 TYR E 98 ARG 0.008 0.001 ARG A 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 812 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 732 time to evaluate : 2.261 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: 0.7747 (OUTLIER) cc_final: 0.7435 (tpt-90) REVERT: D 211 MET cc_start: 0.6994 (ttp) cc_final: 0.6564 (ttm) REVERT: E 179 GLN cc_start: 0.8459 (tp40) cc_final: 0.8249 (tp-100) REVERT: E 211 MET cc_start: 0.7076 (mtp) cc_final: 0.6849 (mtt) REVERT: G 134 GLU cc_start: 0.8343 (pt0) cc_final: 0.7659 (pt0) REVERT: G 189 TRP cc_start: 0.8402 (m100) cc_final: 0.7990 (m100) REVERT: G 206 THR cc_start: 0.8133 (m) cc_final: 0.7802 (p) REVERT: H 59 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: H 87 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6554 (mpt) REVERT: H 176 GLU cc_start: 0.8309 (tp30) cc_final: 0.8053 (tp30) REVERT: H 179 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7902 (tmm-80) REVERT: I 59 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: I 104 PHE cc_start: 0.4379 (OUTLIER) cc_final: 0.3629 (m-80) REVERT: I 146 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.6603 (mmt) REVERT: J 202 ASP cc_start: 0.8559 (m-30) cc_final: 0.8202 (m-30) REVERT: K 104 PHE cc_start: 0.4406 (OUTLIER) cc_final: 0.3685 (m-80) REVERT: K 204 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7858 (tm-30) REVERT: L 59 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: L 60 GLU cc_start: 0.7679 (mp0) cc_final: 0.7233 (mp0) REVERT: L 87 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5841 (mpt) REVERT: M 60 GLU cc_start: 0.7809 (mp0) cc_final: 0.7456 (mp0) REVERT: M 104 PHE cc_start: 0.4209 (OUTLIER) cc_final: 0.3599 (m-80) REVERT: M 179 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8062 (mmm-85) REVERT: M 185 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: M 204 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7910 (tm-30) REVERT: N 59 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: N 164 ARG cc_start: 0.5638 (OUTLIER) cc_final: 0.5242 (ttm110) REVERT: N 202 ASP cc_start: 0.8522 (m-30) cc_final: 0.8165 (m-30) outliers start: 80 outliers final: 50 residues processed: 762 average time/residue: 1.2809 time to fit residues: 1097.8797 Evaluate side-chains 779 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 714 time to evaluate : 2.247 ------------------------------------------------------------------------------- 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 116 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU 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 F residue 134 GLU Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain H residue 59 GLU 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 179 ARG Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU 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 225 SER Chi-restraints excluded: chain J residue 87 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 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE 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 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 220 ILE Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 179 ARG Chi-restraints excluded: chain M residue 185 GLU 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 160 SER Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 164 ARG Chi-restraints excluded: chain N residue 200 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 0.6980 chunk 232 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 chunk 244 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 58 ASN B 179 GLN C 58 ASN C 63 GLN C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 132 ASN F 58 ASN F 138 HIS F 171 GLN F 179 GLN G 38 ASN G 171 GLN G 179 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19460 Z= 0.186 Angle : 0.653 13.566 26369 Z= 0.322 Chirality : 0.042 0.153 3073 Planarity : 0.005 0.041 3451 Dihedral : 4.564 53.223 2711 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.72 % Allowed : 30.14 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.98 (0.18), residues: 2478 helix: 2.34 (0.14), residues: 1358 sheet: 1.55 (0.34), residues: 210 loop : -0.35 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 189 HIS 0.013 0.001 HIS D 138 PHE 0.010 0.001 PHE E 128 TYR 0.015 0.001 TYR D 98 ARG 0.008 0.001 ARG A 182 ********************** 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 799 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 723 time to evaluate : 2.053 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: 0.7743 (OUTLIER) cc_final: 0.7407 (tpt-90) REVERT: D 211 MET cc_start: 0.6979 (ttp) cc_final: 0.6582 (ttm) REVERT: E 211 MET cc_start: 0.7013 (mtp) cc_final: 0.6780 (mtt) REVERT: G 189 TRP cc_start: 0.8402 (m100) cc_final: 0.8069 (m100) REVERT: G 206 THR cc_start: 0.8106 (m) cc_final: 0.7786 (p) REVERT: H 59 GLU cc_start: 0.8218 (mp0) cc_final: 0.7945 (mp0) REVERT: H 87 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6523 (mpt) REVERT: H 176 GLU cc_start: 0.8317 (tp30) cc_final: 0.8117 (tp30) REVERT: H 179 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7975 (tmm-80) REVERT: I 59 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: I 104 PHE cc_start: 0.4433 (OUTLIER) cc_final: 0.3727 (m-80) REVERT: J 202 ASP cc_start: 0.8500 (m-30) cc_final: 0.8158 (m-30) REVERT: K 104 PHE cc_start: 0.4210 (OUTLIER) cc_final: 0.3505 (m-80) REVERT: K 204 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7838 (tm-30) REVERT: L 59 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: L 60 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: L 87 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5849 (mpt) REVERT: M 60 GLU cc_start: 0.7798 (mp0) cc_final: 0.7456 (mp0) REVERT: M 104 PHE cc_start: 0.4290 (OUTLIER) cc_final: 0.3733 (m-80) REVERT: M 185 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: N 59 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: N 202 ASP cc_start: 0.8514 (m-30) cc_final: 0.8136 (m-30) outliers start: 76 outliers final: 49 residues processed: 752 average time/residue: 1.2339 time to fit residues: 1041.0241 Evaluate side-chains 786 residues out of total 2044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 725 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 116 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain D residue 43 GLU 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 E residue 120 SER Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 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 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 179 ARG Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 104 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 225 SER Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 187 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 68 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 104 PHE 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 87 MET Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 152 ARG Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 104 PHE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 185 GLU 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 141 THR Chi-restraints excluded: chain N residue 220 ILE 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: 8.9990 chunk 207 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 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 171 GLN A 179 GLN B 171 GLN B 179 GLN C 58 ASN C 63 GLN C 132 ASN C 138 HIS C 179 GLN D 58 ASN D 138 HIS D 179 GLN E 132 ASN E 179 GLN F 58 ASN F 138 HIS F 171 GLN F 179 GLN G 38 ASN G 171 GLN G 179 GLN I 75 ASN K 75 ASN K 98 ASN L 75 ASN L 156 HIS L 175 ASN M 75 ASN N 75 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.113236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103978 restraints weight = 28262.182| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.80 r_work: 0.3496 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19460 Z= 0.214 Angle : 0.666 13.748 26369 Z= 0.330 Chirality : 0.043 0.156 3073 Planarity : 0.005 0.038 3451 Dihedral : 4.598 54.039 2711 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.57 % Allowed : 31.16 % Favored : 65.26 % 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: 2.29 (0.14), residues: 1358 sheet: 1.35 (0.34), residues: 217 loop : -0.38 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 189 HIS 0.016 0.001 HIS D 138 PHE 0.013 0.001 PHE N 104 TYR 0.019 0.001 TYR E 98 ARG 0.007 0.001 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13796.57 seconds wall clock time: 241 minutes 12.57 seconds (14472.57 seconds total)