Starting phenix.real_space_refine on Mon Feb 19 18:27:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/02_2024/7pv2_13664.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/02_2024/7pv2_13664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/02_2024/7pv2_13664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/02_2024/7pv2_13664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/02_2024/7pv2_13664.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv2_13664/02_2024/7pv2_13664.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 108 5.16 5 C 16476 2.51 5 N 4176 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 59": "NH1" <-> "NH2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E ARG 263": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 196": "OD1" <-> "OD2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "G ARG 59": "NH1" <-> "NH2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G ARG 263": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 196": "OD1" <-> "OD2" Residue "H ARG 263": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 109": "OD1" <-> "OD2" Residue "I ASP 113": "OD1" <-> "OD2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 196": "OD1" <-> "OD2" Residue "I ARG 263": "NH1" <-> "NH2" Residue "J ARG 59": "NH1" <-> "NH2" Residue "J PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 109": "OD1" <-> "OD2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 196": "OD1" <-> "OD2" Residue "J ARG 263": "NH1" <-> "NH2" Residue "K ARG 59": "NH1" <-> "NH2" Residue "K PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 109": "OD1" <-> "OD2" Residue "K ASP 113": "OD1" <-> "OD2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 196": "OD1" <-> "OD2" Residue "K ARG 263": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 109": "OD1" <-> "OD2" Residue "L ASP 113": "OD1" <-> "OD2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 196": "OD1" <-> "OD2" Residue "L ARG 263": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25440 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "C" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "D" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "E" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "F" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "H" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "I" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "J" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "K" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "L" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2120 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Time building chain proxies: 12.73, per 1000 atoms: 0.50 Number of scatterers: 25440 At special positions: 0 Unit cell: (167.99, 167.99, 88.81, 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 108 16.00 O 4680 8.00 N 4176 7.00 C 16476 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: 8.93 Conformation dependent library (CDL) restraints added in 4.0 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 48 sheets defined 42.4% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.675A pdb=" N PHE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 Proline residue: A 262 - end of helix Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 141 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 274 Proline residue: B 262 - end of helix Processing helix chain 'C' and resid 10 through 16 removed outlier: 3.630A pdb=" N ILE C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 228 removed outlier: 3.677A pdb=" N PHE C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 274 Proline residue: C 262 - end of helix Processing helix chain 'D' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 274 Proline residue: D 262 - end of helix Processing helix chain 'E' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE E 14 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR E 177 " --> pdb=" O MET E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 274 Proline residue: E 262 - end of helix Processing helix chain 'F' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE F 14 " --> pdb=" O THR F 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 36 removed outlier: 3.849A pdb=" N ARG F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU F 136 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET F 141 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR F 177 " --> pdb=" O MET F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 274 Proline residue: F 262 - end of helix Processing helix chain 'G' and resid 10 through 16 removed outlier: 3.632A pdb=" N ILE G 14 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG G 16 " --> pdb=" O GLY G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU G 138 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR G 177 " --> pdb=" O MET G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 274 Proline residue: G 262 - end of helix Processing helix chain 'H' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE H 14 " --> pdb=" O THR H 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG H 24 " --> pdb=" O ASN H 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 60 Processing helix chain 'H' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU H 138 " --> pdb=" O ASP H 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR H 177 " --> pdb=" O MET H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 274 Proline residue: H 262 - end of helix Processing helix chain 'I' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE I 14 " --> pdb=" O THR I 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG I 16 " --> pdb=" O GLY I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG I 24 " --> pdb=" O ASN I 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 60 Processing helix chain 'I' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU I 136 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU I 138 " --> pdb=" O ASP I 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET I 141 " --> pdb=" O ASN I 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET I 173 " --> pdb=" O ASP I 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR I 177 " --> pdb=" O MET I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 228 removed outlier: 3.677A pdb=" N PHE I 216 " --> pdb=" O LEU I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 274 Proline residue: I 262 - end of helix Processing helix chain 'J' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE J 14 " --> pdb=" O THR J 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG J 16 " --> pdb=" O GLY J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 36 removed outlier: 3.847A pdb=" N ARG J 24 " --> pdb=" O ASN J 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 60 Processing helix chain 'J' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET J 141 " --> pdb=" O ASN J 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET J 173 " --> pdb=" O ASP J 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR J 177 " --> pdb=" O MET J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 228 removed outlier: 3.675A pdb=" N PHE J 216 " --> pdb=" O LEU J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 274 Proline residue: J 262 - end of helix Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.632A pdb=" N ILE K 14 " --> pdb=" O THR K 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG K 24 " --> pdb=" O ASN K 20 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 132 through 155 removed outlier: 3.726A pdb=" N LEU K 136 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET K 141 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 177 removed outlier: 3.724A pdb=" N MET K 173 " --> pdb=" O ASP K 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR K 177 " --> pdb=" O MET K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE K 216 " --> pdb=" O LEU K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 274 Proline residue: K 262 - end of helix Processing helix chain 'L' and resid 10 through 16 removed outlier: 3.631A pdb=" N ILE L 14 " --> pdb=" O THR L 10 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 36 removed outlier: 3.848A pdb=" N ARG L 24 " --> pdb=" O ASN L 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 60 Processing helix chain 'L' and resid 132 through 155 removed outlier: 3.727A pdb=" N LEU L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU L 138 " --> pdb=" O ASP L 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET L 141 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR L 151 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 177 removed outlier: 3.725A pdb=" N MET L 173 " --> pdb=" O ASP L 169 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL L 176 " --> pdb=" O SER L 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 228 removed outlier: 3.676A pdb=" N PHE L 216 " --> pdb=" O LEU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 274 Proline residue: L 262 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS A 281 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 279 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL A 161 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE B 188 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 163 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.150A pdb=" N VAL A 186 " --> pdb=" O VAL L 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS B 281 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 279 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL B 161 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE C 188 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 163 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS C 281 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 279 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 202 removed outlier: 7.170A pdb=" N VAL C 161 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE D 188 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 163 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS D 281 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 279 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 74 through 75 Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AB8, first strand: chain 'D' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL D 161 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE E 188 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 163 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS E 281 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 279 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC3, first strand: chain 'E' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL E 161 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE F 188 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 163 " --> pdb=" O PHE F 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS F 281 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER F 279 " --> pdb=" O GLN F 41 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AC6, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'F' and resid 199 through 202 removed outlier: 7.248A pdb=" N VAL F 161 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N PHE G 188 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 163 " --> pdb=" O PHE G 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS G 281 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER G 279 " --> pdb=" O GLN G 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AD2, first strand: chain 'G' and resid 199 through 202 removed outlier: 4.220A pdb=" N VAL H 186 " --> pdb=" O VAL G 161 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS H 281 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 279 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AD5, first strand: chain 'H' and resid 91 through 93 Processing sheet with id=AD6, first strand: chain 'H' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL H 161 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE I 188 " --> pdb=" O VAL H 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE H 163 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS I 281 " --> pdb=" O GLU I 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER I 279 " --> pdb=" O GLN I 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 74 through 75 Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 93 Processing sheet with id=AE1, first strand: chain 'I' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL I 161 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE J 188 " --> pdb=" O VAL I 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE I 163 " --> pdb=" O PHE J 188 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 38 through 41 removed outlier: 3.503A pdb=" N LYS J 281 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER J 279 " --> pdb=" O GLN J 41 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AE4, first strand: chain 'J' and resid 91 through 93 Processing sheet with id=AE5, first strand: chain 'J' and resid 199 through 202 removed outlier: 7.172A pdb=" N VAL J 161 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N PHE K 188 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE J 163 " --> pdb=" O PHE K 188 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS K 281 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER K 279 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AE8, first strand: chain 'K' and resid 91 through 93 Processing sheet with id=AE9, first strand: chain 'K' and resid 199 through 202 removed outlier: 7.171A pdb=" N VAL K 161 " --> pdb=" O VAL L 186 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N PHE L 188 " --> pdb=" O VAL K 161 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE K 163 " --> pdb=" O PHE L 188 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 38 through 41 removed outlier: 3.502A pdb=" N LYS L 281 " --> pdb=" O GLU L 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 279 " --> pdb=" O GLN L 41 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 74 through 75 Processing sheet with id=AF3, first strand: chain 'L' and resid 91 through 93 966 hydrogen bonds defined for protein. 2826 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: 7.20 Time building geometry restraints manager: 9.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8053 1.34 - 1.46: 6031 1.46 - 1.57: 11764 1.57 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 26052 Sorted by residual: bond pdb=" CB ILE A 150 " pdb=" CG2 ILE A 150 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.83e+00 bond pdb=" CB ILE D 150 " pdb=" CG2 ILE D 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CB ILE E 150 " pdb=" CG2 ILE E 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CB ILE B 150 " pdb=" CG2 ILE B 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" CB ILE H 150 " pdb=" CG2 ILE H 150 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 26047 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.35: 408 105.35 - 112.53: 12270 112.53 - 119.71: 9330 119.71 - 126.89: 12950 126.89 - 134.06: 274 Bond angle restraints: 35232 Sorted by residual: angle pdb=" CA GLY E 190 " pdb=" C GLY E 190 " pdb=" O GLY E 190 " ideal model delta sigma weight residual 122.37 120.45 1.92 7.30e-01 1.88e+00 6.94e+00 angle pdb=" CA GLY H 190 " pdb=" C GLY H 190 " pdb=" O GLY H 190 " ideal model delta sigma weight residual 122.37 120.45 1.92 7.30e-01 1.88e+00 6.94e+00 angle pdb=" CA GLY D 190 " pdb=" C GLY D 190 " pdb=" O GLY D 190 " ideal model delta sigma weight residual 122.37 120.47 1.90 7.30e-01 1.88e+00 6.79e+00 angle pdb=" CA GLY B 190 " pdb=" C GLY B 190 " pdb=" O GLY B 190 " ideal model delta sigma weight residual 122.37 120.47 1.90 7.30e-01 1.88e+00 6.75e+00 angle pdb=" CA GLY J 190 " pdb=" C GLY J 190 " pdb=" O GLY J 190 " ideal model delta sigma weight residual 122.37 120.48 1.89 7.30e-01 1.88e+00 6.73e+00 ... (remaining 35227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 13368 15.55 - 31.09: 1692 31.09 - 46.64: 223 46.64 - 62.19: 101 62.19 - 77.74: 84 Dihedral angle restraints: 15468 sinusoidal: 6396 harmonic: 9072 Sorted by residual: dihedral pdb=" CA LEU L 73 " pdb=" C LEU L 73 " pdb=" N GLY L 74 " pdb=" CA GLY L 74 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA LEU F 73 " pdb=" C LEU F 73 " pdb=" N GLY F 74 " pdb=" CA GLY F 74 " ideal model delta harmonic sigma weight residual 180.00 163.81 16.19 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA LEU I 73 " pdb=" C LEU I 73 " pdb=" N GLY I 74 " pdb=" CA GLY I 74 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 15465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3090 0.086 - 0.171: 383 0.171 - 0.257: 108 0.257 - 0.343: 79 0.343 - 0.428: 24 Chirality restraints: 3684 Sorted by residual: chirality pdb=" CB ILE A 135 " pdb=" CA ILE A 135 " pdb=" CG1 ILE A 135 " pdb=" CG2 ILE A 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE K 135 " pdb=" CA ILE K 135 " pdb=" CG1 ILE K 135 " pdb=" CG2 ILE K 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE E 135 " pdb=" CA ILE E 135 " pdb=" CG1 ILE E 135 " pdb=" CG2 ILE E 135 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 3681 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN J 251 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" CD GLN J 251 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN J 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN J 251 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 251 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" CD GLN A 251 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN A 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN A 251 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 251 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" CD GLN H 251 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN H 251 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN H 251 " -0.014 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 205 2.56 - 3.14: 20668 3.14 - 3.73: 35405 3.73 - 4.31: 51075 4.31 - 4.90: 88641 Nonbonded interactions: 195994 Sorted by model distance: nonbonded pdb=" OD1 ASP J 169 " pdb=" OG SER J 172 " model vdw 1.971 2.440 nonbonded pdb=" OD1 ASP B 169 " pdb=" OG SER B 172 " model vdw 1.971 2.440 nonbonded pdb=" OD1 ASP K 169 " pdb=" OG SER K 172 " model vdw 1.971 2.440 nonbonded pdb=" OD1 ASP D 169 " pdb=" OG SER D 172 " model vdw 1.971 2.440 nonbonded pdb=" OD1 ASP F 169 " pdb=" OG SER F 172 " model vdw 1.971 2.440 ... (remaining 195989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 7.300 Check model and map are aligned: 0.430 Set scattering table: 0.220 Process input model: 60.380 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.170 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.011 0.070 26052 Z= 0.695 Angle : 0.714 7.019 35232 Z= 0.392 Chirality : 0.084 0.428 3684 Planarity : 0.004 0.039 4536 Dihedral : 14.851 77.735 9708 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -3.84 (0.12), residues: 3036 helix: -1.58 (0.13), residues: 1272 sheet: -3.39 (0.35), residues: 144 loop : -3.41 (0.11), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 22 HIS 0.001 0.000 HIS I 57 PHE 0.011 0.002 PHE L 64 TYR 0.012 0.002 TYR L 273 ARG 0.007 0.001 ARG L 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8329 (pptt) cc_final: 0.7836 (pptt) REVERT: E 45 LYS cc_start: 0.8272 (pptt) cc_final: 0.7783 (pptt) REVERT: E 155 ASN cc_start: 0.8270 (t0) cc_final: 0.8022 (t0) REVERT: H 45 LYS cc_start: 0.8037 (pptt) cc_final: 0.7702 (pptt) REVERT: H 207 TYR cc_start: 0.8691 (t80) cc_final: 0.7627 (t80) REVERT: J 69 MET cc_start: 0.7164 (ttt) cc_final: 0.6883 (tmm) REVERT: K 45 LYS cc_start: 0.8272 (pptt) cc_final: 0.8016 (pptt) REVERT: K 207 TYR cc_start: 0.8806 (t80) cc_final: 0.7950 (t80) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.4033 time to fit residues: 299.2282 Evaluate side-chains 380 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 0.0980 chunk 121 optimal weight: 0.8980 chunk 235 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 chunk 175 optimal weight: 0.4980 chunk 272 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN B 155 ASN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN D 36 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 58 GLN G 155 ASN ** G 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** H 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN ** I 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 GLN ** J 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 26052 Z= 0.131 Angle : 0.494 7.321 35232 Z= 0.252 Chirality : 0.043 0.141 3684 Planarity : 0.003 0.036 4536 Dihedral : 3.723 18.896 3432 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.52 % Allowed : 6.85 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.14), residues: 3036 helix: -0.25 (0.15), residues: 1296 sheet: -2.93 (0.37), residues: 144 loop : -2.50 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 40 HIS 0.001 0.000 HIS J 57 PHE 0.009 0.001 PHE D 216 TYR 0.015 0.001 TYR G 92 ARG 0.002 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 429 time to evaluate : 2.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8221 (pptt) cc_final: 0.7745 (pptt) REVERT: C 214 MET cc_start: 0.7103 (mmm) cc_final: 0.6868 (mmm) REVERT: H 207 TYR cc_start: 0.8839 (t80) cc_final: 0.7993 (t80) REVERT: K 73 LEU cc_start: 0.7784 (tp) cc_final: 0.7581 (tt) REVERT: K 207 TYR cc_start: 0.8919 (t80) cc_final: 0.8178 (t80) outliers start: 14 outliers final: 4 residues processed: 433 average time/residue: 0.4317 time to fit residues: 286.0484 Evaluate side-chains 393 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 389 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain L residue 167 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 272 optimal weight: 0.0060 chunk 294 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 218 optimal weight: 0.0370 overall best weight: 1.1878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26052 Z= 0.180 Angle : 0.473 4.760 35232 Z= 0.247 Chirality : 0.043 0.151 3684 Planarity : 0.003 0.029 4536 Dihedral : 3.660 18.363 3432 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.00 % Allowed : 7.52 % Favored : 91.48 % 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: -1.53 (0.15), residues: 3036 helix: 0.25 (0.15), residues: 1296 sheet: -2.69 (0.39), residues: 144 loop : -1.99 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 40 HIS 0.002 0.000 HIS D 57 PHE 0.012 0.001 PHE F 64 TYR 0.017 0.001 TYR E 70 ARG 0.003 0.000 ARG G 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 396 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 LEU cc_start: 0.2352 (OUTLIER) cc_final: 0.1589 (pp) REVERT: C 114 LEU cc_start: 0.2967 (OUTLIER) cc_final: 0.2651 (pp) REVERT: C 214 MET cc_start: 0.7540 (mmm) cc_final: 0.7217 (mmm) REVERT: D 45 LYS cc_start: 0.8108 (pptt) cc_final: 0.7707 (pttp) REVERT: E 45 LYS cc_start: 0.8126 (pptt) cc_final: 0.7742 (pptt) REVERT: E 114 LEU cc_start: 0.2151 (OUTLIER) cc_final: 0.1443 (pp) REVERT: F 114 LEU cc_start: 0.2603 (OUTLIER) cc_final: 0.2247 (pp) REVERT: G 45 LYS cc_start: 0.8370 (pttp) cc_final: 0.8115 (pttp) REVERT: G 114 LEU cc_start: 0.2328 (OUTLIER) cc_final: 0.1495 (pp) REVERT: H 114 LEU cc_start: 0.2597 (OUTLIER) cc_final: 0.1814 (pp) REVERT: I 114 LEU cc_start: 0.3003 (OUTLIER) cc_final: 0.2616 (pp) REVERT: J 43 LEU cc_start: 0.8924 (mp) cc_final: 0.8688 (mt) REVERT: J 110 MET cc_start: 0.7379 (ptm) cc_final: 0.7163 (ptm) REVERT: J 141 MET cc_start: 0.7811 (ptt) cc_final: 0.7603 (ptt) REVERT: K 45 LYS cc_start: 0.8164 (pptt) cc_final: 0.7858 (pptt) REVERT: K 85 LEU cc_start: 0.8116 (tp) cc_final: 0.7686 (mm) REVERT: K 114 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2053 (pp) REVERT: L 114 LEU cc_start: 0.3046 (OUTLIER) cc_final: 0.2626 (pp) outliers start: 27 outliers final: 9 residues processed: 414 average time/residue: 0.4348 time to fit residues: 266.7159 Evaluate side-chains 380 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 362 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 273 optimal weight: 0.7980 chunk 289 optimal weight: 0.6980 chunk 143 optimal weight: 0.0870 chunk 259 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN G 271 ASN ** H 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26052 Z= 0.157 Angle : 0.455 5.985 35232 Z= 0.237 Chirality : 0.042 0.144 3684 Planarity : 0.003 0.027 4536 Dihedral : 3.651 19.106 3432 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.41 % Allowed : 7.81 % Favored : 90.78 % 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: -1.11 (0.15), residues: 3036 helix: 0.53 (0.15), residues: 1308 sheet: -2.43 (0.43), residues: 144 loop : -1.70 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 40 HIS 0.001 0.000 HIS G 57 PHE 0.011 0.001 PHE H 64 TYR 0.012 0.001 TYR E 8 ARG 0.004 0.000 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 383 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7911 (pt0) cc_final: 0.7695 (pp30) REVERT: A 45 LYS cc_start: 0.8233 (pptt) cc_final: 0.7707 (pptt) REVERT: A 70 TYR cc_start: 0.6697 (m-80) cc_final: 0.6459 (m-80) REVERT: B 24 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7331 (mtm110) REVERT: B 85 LEU cc_start: 0.8210 (tp) cc_final: 0.7862 (mm) REVERT: B 114 LEU cc_start: 0.2532 (OUTLIER) cc_final: 0.1772 (pp) REVERT: C 114 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2355 (pp) REVERT: C 214 MET cc_start: 0.7620 (mmm) cc_final: 0.7238 (mmt) REVERT: D 33 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9077 (tp) REVERT: D 45 LYS cc_start: 0.8160 (pptt) cc_final: 0.7751 (pttp) REVERT: E 45 LYS cc_start: 0.8153 (pptt) cc_final: 0.7753 (pptt) REVERT: E 114 LEU cc_start: 0.2347 (OUTLIER) cc_final: 0.1659 (pp) REVERT: E 130 MET cc_start: 0.8752 (ttp) cc_final: 0.8516 (ttp) REVERT: E 224 MET cc_start: 0.8525 (mmp) cc_final: 0.8275 (mmp) REVERT: F 114 LEU cc_start: 0.3224 (OUTLIER) cc_final: 0.2781 (pp) REVERT: G 45 LYS cc_start: 0.8343 (pttp) cc_final: 0.8061 (pttp) REVERT: G 70 TYR cc_start: 0.6529 (m-80) cc_final: 0.6289 (m-80) REVERT: H 114 LEU cc_start: 0.2762 (OUTLIER) cc_final: 0.1983 (pp) REVERT: I 114 LEU cc_start: 0.3184 (OUTLIER) cc_final: 0.2764 (pp) REVERT: J 45 LYS cc_start: 0.8217 (pptt) cc_final: 0.7552 (pptt) REVERT: K 36 GLN cc_start: 0.7906 (pt0) cc_final: 0.7617 (pp30) REVERT: K 45 LYS cc_start: 0.8201 (pptt) cc_final: 0.7839 (pptt) REVERT: K 85 LEU cc_start: 0.8213 (tp) cc_final: 0.7865 (mm) REVERT: K 114 LEU cc_start: 0.2831 (OUTLIER) cc_final: 0.2026 (pp) REVERT: K 224 MET cc_start: 0.8443 (mmp) cc_final: 0.8242 (mmp) REVERT: L 114 LEU cc_start: 0.3127 (OUTLIER) cc_final: 0.2668 (pp) REVERT: L 181 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7006 (mt-10) outliers start: 38 outliers final: 15 residues processed: 407 average time/residue: 0.4296 time to fit residues: 260.6040 Evaluate side-chains 373 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 348 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain H residue 167 ASP Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 5.9990 chunk 164 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN G 82 GLN ** H 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 271 ASN ** K 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26052 Z= 0.274 Angle : 0.518 6.822 35232 Z= 0.272 Chirality : 0.045 0.151 3684 Planarity : 0.003 0.026 4536 Dihedral : 3.954 18.351 3432 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.93 % Allowed : 9.59 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3036 helix: 0.73 (0.15), residues: 1272 sheet: -2.43 (0.44), residues: 144 loop : -1.51 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 22 HIS 0.001 0.001 HIS F 57 PHE 0.016 0.002 PHE H 64 TYR 0.014 0.001 TYR H 92 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 399 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8316 (pptt) cc_final: 0.7795 (pptt) REVERT: B 85 LEU cc_start: 0.8420 (tp) cc_final: 0.8104 (mm) REVERT: B 114 LEU cc_start: 0.2606 (OUTLIER) cc_final: 0.1970 (pp) REVERT: B 224 MET cc_start: 0.8617 (mmp) cc_final: 0.8295 (mmp) REVERT: C 114 LEU cc_start: 0.2942 (OUTLIER) cc_final: 0.2354 (pp) REVERT: C 214 MET cc_start: 0.7704 (mmm) cc_final: 0.7463 (mmm) REVERT: D 33 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9134 (tp) REVERT: D 45 LYS cc_start: 0.8256 (pptt) cc_final: 0.7755 (pptt) REVERT: E 85 LEU cc_start: 0.8524 (tp) cc_final: 0.8234 (mm) REVERT: E 114 LEU cc_start: 0.2581 (OUTLIER) cc_final: 0.1841 (pp) REVERT: E 224 MET cc_start: 0.8631 (mmp) cc_final: 0.8360 (mmp) REVERT: F 114 LEU cc_start: 0.3052 (OUTLIER) cc_final: 0.2340 (pp) REVERT: G 70 TYR cc_start: 0.6532 (m-80) cc_final: 0.6317 (m-80) REVERT: H 45 LYS cc_start: 0.8198 (pptt) cc_final: 0.7575 (pptt) REVERT: H 85 LEU cc_start: 0.8371 (tp) cc_final: 0.8099 (mm) REVERT: H 114 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.1904 (pp) REVERT: I 114 LEU cc_start: 0.3297 (OUTLIER) cc_final: 0.2487 (pp) REVERT: J 45 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8081 (pttp) REVERT: J 109 ASP cc_start: 0.6587 (t0) cc_final: 0.6191 (t0) REVERT: K 45 LYS cc_start: 0.8184 (pptt) cc_final: 0.7664 (pptt) REVERT: K 85 LEU cc_start: 0.8466 (tp) cc_final: 0.8155 (mm) REVERT: K 114 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2054 (pp) REVERT: L 85 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8148 (tp) REVERT: L 109 ASP cc_start: 0.6553 (t0) cc_final: 0.6230 (t0) REVERT: L 114 LEU cc_start: 0.3252 (OUTLIER) cc_final: 0.2500 (pp) REVERT: L 181 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7087 (tt0) outliers start: 52 outliers final: 18 residues processed: 430 average time/residue: 0.4275 time to fit residues: 274.1788 Evaluate side-chains 337 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 307 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 290 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 134 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 82 GLN B 271 ASN D 271 ASN E 82 GLN E 271 ASN F 82 GLN G 82 GLN H 271 ASN I 82 GLN I 271 ASN K 271 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26052 Z= 0.128 Angle : 0.450 6.406 35232 Z= 0.235 Chirality : 0.041 0.135 3684 Planarity : 0.002 0.027 4536 Dihedral : 3.723 18.369 3432 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.74 % Allowed : 10.07 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3036 helix: 0.93 (0.15), residues: 1296 sheet: -2.38 (0.44), residues: 144 loop : -1.24 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 22 HIS 0.001 0.000 HIS J 57 PHE 0.009 0.001 PHE F 64 TYR 0.018 0.001 TYR G 92 ARG 0.003 0.000 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 344 time to evaluate : 3.116 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8198 (pptt) cc_final: 0.7787 (pttp) REVERT: B 85 LEU cc_start: 0.8484 (tp) cc_final: 0.8139 (mm) REVERT: B 114 LEU cc_start: 0.2783 (OUTLIER) cc_final: 0.2118 (pp) REVERT: C 109 ASP cc_start: 0.6550 (t0) cc_final: 0.6027 (t0) REVERT: C 114 LEU cc_start: 0.3018 (OUTLIER) cc_final: 0.2518 (pp) REVERT: C 141 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7640 (ptt) REVERT: D 33 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9103 (tp) REVERT: D 45 LYS cc_start: 0.8172 (pptt) cc_final: 0.7647 (pptt) REVERT: E 83 ILE cc_start: 0.8825 (pt) cc_final: 0.8618 (pt) REVERT: E 85 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8114 (mm) REVERT: E 114 LEU cc_start: 0.2628 (OUTLIER) cc_final: 0.1998 (pp) REVERT: F 114 LEU cc_start: 0.3070 (OUTLIER) cc_final: 0.2388 (pp) REVERT: H 114 LEU cc_start: 0.2722 (OUTLIER) cc_final: 0.2041 (pp) REVERT: I 114 LEU cc_start: 0.3170 (OUTLIER) cc_final: 0.2516 (pp) REVERT: I 141 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7519 (ptt) REVERT: J 45 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8104 (pttp) REVERT: K 45 LYS cc_start: 0.8197 (pptt) cc_final: 0.7808 (pptt) REVERT: K 85 LEU cc_start: 0.8499 (tp) cc_final: 0.8161 (mm) REVERT: K 114 LEU cc_start: 0.2763 (OUTLIER) cc_final: 0.2046 (pp) REVERT: L 85 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8223 (tp) REVERT: L 114 LEU cc_start: 0.3125 (OUTLIER) cc_final: 0.2461 (pp) REVERT: L 141 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7609 (ptt) outliers start: 47 outliers final: 16 residues processed: 377 average time/residue: 0.4543 time to fit residues: 250.8026 Evaluate side-chains 347 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 316 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 289 optimal weight: 0.0770 chunk 180 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 82 GLN C 82 GLN E 82 GLN F 82 GLN G 15 GLN G 82 GLN I 82 GLN J 15 GLN J 82 GLN L 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26052 Z= 0.164 Angle : 0.464 8.296 35232 Z= 0.242 Chirality : 0.042 0.158 3684 Planarity : 0.003 0.026 4536 Dihedral : 3.685 17.945 3432 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.67 % Allowed : 10.59 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3036 helix: 1.09 (0.15), residues: 1296 sheet: -2.29 (0.45), residues: 144 loop : -1.10 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 22 HIS 0.001 0.000 HIS D 57 PHE 0.011 0.001 PHE G 64 TYR 0.021 0.001 TYR H 92 ARG 0.004 0.000 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 328 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8235 (pptt) cc_final: 0.7823 (pttp) REVERT: B 114 LEU cc_start: 0.2796 (OUTLIER) cc_final: 0.2125 (pp) REVERT: C 114 LEU cc_start: 0.2931 (OUTLIER) cc_final: 0.2380 (pp) REVERT: D 33 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9111 (tp) REVERT: D 45 LYS cc_start: 0.8178 (pptt) cc_final: 0.7752 (pttp) REVERT: E 114 LEU cc_start: 0.2617 (OUTLIER) cc_final: 0.1999 (pp) REVERT: F 114 LEU cc_start: 0.3116 (OUTLIER) cc_final: 0.2452 (pp) REVERT: F 141 MET cc_start: 0.7957 (ptt) cc_final: 0.7697 (ptt) REVERT: H 114 LEU cc_start: 0.2894 (OUTLIER) cc_final: 0.2235 (pp) REVERT: I 114 LEU cc_start: 0.3118 (OUTLIER) cc_final: 0.2448 (pp) REVERT: K 45 LYS cc_start: 0.8219 (pptt) cc_final: 0.7807 (pptt) REVERT: K 114 LEU cc_start: 0.2811 (OUTLIER) cc_final: 0.2105 (pp) REVERT: L 85 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8264 (tp) REVERT: L 114 LEU cc_start: 0.3210 (OUTLIER) cc_final: 0.2555 (pp) REVERT: L 141 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7772 (ptt) outliers start: 45 outliers final: 21 residues processed: 361 average time/residue: 0.4364 time to fit residues: 229.1061 Evaluate side-chains 346 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 314 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 82 GLN C 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN I 82 GLN J 82 GLN K 82 GLN L 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 26052 Z= 0.388 Angle : 0.578 7.884 35232 Z= 0.302 Chirality : 0.047 0.152 3684 Planarity : 0.003 0.023 4536 Dihedral : 4.103 18.079 3432 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.11 % Allowed : 11.07 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3036 helix: 0.88 (0.15), residues: 1284 sheet: -2.29 (0.46), residues: 144 loop : -1.19 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 22 HIS 0.002 0.001 HIS C 57 PHE 0.019 0.002 PHE E 64 TYR 0.016 0.002 TYR B 108 ARG 0.005 0.000 ARG I 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 311 time to evaluate : 2.887 Fit side-chains REVERT: A 45 LYS cc_start: 0.8354 (pptt) cc_final: 0.7937 (pttp) REVERT: B 114 LEU cc_start: 0.2913 (OUTLIER) cc_final: 0.2022 (pp) REVERT: C 114 LEU cc_start: 0.3103 (OUTLIER) cc_final: 0.2344 (pp) REVERT: D 45 LYS cc_start: 0.8329 (pptt) cc_final: 0.7879 (pttp) REVERT: E 114 LEU cc_start: 0.2737 (OUTLIER) cc_final: 0.2109 (pp) REVERT: E 214 MET cc_start: 0.7903 (mmm) cc_final: 0.7654 (mmm) REVERT: F 114 LEU cc_start: 0.3082 (OUTLIER) cc_final: 0.2434 (pp) REVERT: H 45 LYS cc_start: 0.8270 (pptt) cc_final: 0.7655 (pptt) REVERT: H 114 LEU cc_start: 0.2898 (OUTLIER) cc_final: 0.2119 (pp) REVERT: I 114 LEU cc_start: 0.3197 (OUTLIER) cc_final: 0.2489 (pp) REVERT: K 45 LYS cc_start: 0.8230 (pptt) cc_final: 0.7671 (pptt) REVERT: K 85 LEU cc_start: 0.8547 (tp) cc_final: 0.8215 (mm) REVERT: K 114 LEU cc_start: 0.2731 (OUTLIER) cc_final: 0.1934 (pp) REVERT: L 85 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8299 (tp) REVERT: L 114 LEU cc_start: 0.3263 (OUTLIER) cc_final: 0.2537 (pp) REVERT: L 181 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7097 (tt0) outliers start: 57 outliers final: 30 residues processed: 355 average time/residue: 0.5062 time to fit residues: 259.4286 Evaluate side-chains 312 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 181 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 211 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 243 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 chunk 268 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 82 GLN C 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN I 82 GLN J 82 GLN K 82 GLN L 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26052 Z= 0.144 Angle : 0.470 7.961 35232 Z= 0.245 Chirality : 0.041 0.154 3684 Planarity : 0.003 0.026 4536 Dihedral : 3.864 18.703 3432 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.81 % Allowed : 11.33 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3036 helix: 1.14 (0.15), residues: 1296 sheet: -2.22 (0.46), residues: 144 loop : -1.01 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 40 HIS 0.001 0.000 HIS D 57 PHE 0.009 0.001 PHE C 64 TYR 0.016 0.001 TYR H 92 ARG 0.004 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 307 time to evaluate : 2.826 Fit side-chains REVERT: A 45 LYS cc_start: 0.8266 (pptt) cc_final: 0.7872 (pttp) REVERT: B 85 LEU cc_start: 0.8534 (tp) cc_final: 0.8192 (mm) REVERT: B 114 LEU cc_start: 0.2879 (OUTLIER) cc_final: 0.2194 (pp) REVERT: C 114 LEU cc_start: 0.3065 (OUTLIER) cc_final: 0.2328 (pp) REVERT: D 33 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9113 (tp) REVERT: D 45 LYS cc_start: 0.8220 (pptt) cc_final: 0.7823 (pttp) REVERT: E 114 LEU cc_start: 0.2816 (OUTLIER) cc_final: 0.2203 (pp) REVERT: F 114 LEU cc_start: 0.3128 (OUTLIER) cc_final: 0.2519 (pp) REVERT: F 221 ASN cc_start: 0.8358 (m-40) cc_final: 0.8087 (m-40) REVERT: H 45 LYS cc_start: 0.8170 (pptt) cc_final: 0.7562 (pptt) REVERT: H 114 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2214 (pp) REVERT: I 114 LEU cc_start: 0.3193 (OUTLIER) cc_final: 0.2591 (pp) REVERT: K 45 LYS cc_start: 0.8228 (pptt) cc_final: 0.7750 (pptt) REVERT: K 85 LEU cc_start: 0.8565 (tp) cc_final: 0.8222 (mm) REVERT: K 114 LEU cc_start: 0.2854 (OUTLIER) cc_final: 0.2178 (pp) REVERT: L 85 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8308 (tp) REVERT: L 114 LEU cc_start: 0.3144 (OUTLIER) cc_final: 0.2522 (pp) REVERT: L 141 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7805 (ptt) outliers start: 49 outliers final: 22 residues processed: 342 average time/residue: 0.4969 time to fit residues: 243.2561 Evaluate side-chains 324 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 141 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.8980 chunk 284 optimal weight: 0.9990 chunk 173 optimal weight: 0.1980 chunk 135 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 298 optimal weight: 0.5980 chunk 275 optimal weight: 8.9990 chunk 237 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 82 GLN C 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN I 82 GLN J 82 GLN K 82 GLN L 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26052 Z= 0.132 Angle : 0.461 7.926 35232 Z= 0.241 Chirality : 0.041 0.150 3684 Planarity : 0.003 0.028 4536 Dihedral : 3.725 19.265 3432 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.56 % Allowed : 11.74 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 3036 helix: 1.25 (0.15), residues: 1308 sheet: -2.15 (0.45), residues: 144 loop : -0.87 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 40 HIS 0.001 0.000 HIS D 57 PHE 0.008 0.001 PHE H 64 TYR 0.018 0.001 TYR H 92 ARG 0.004 0.000 ARG F 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 303 time to evaluate : 2.681 Fit side-chains REVERT: A 45 LYS cc_start: 0.8235 (pptt) cc_final: 0.7822 (pttp) REVERT: B 85 LEU cc_start: 0.8505 (tp) cc_final: 0.8151 (mm) REVERT: B 114 LEU cc_start: 0.2905 (OUTLIER) cc_final: 0.2222 (pp) REVERT: C 114 LEU cc_start: 0.3026 (OUTLIER) cc_final: 0.2409 (pp) REVERT: D 45 LYS cc_start: 0.8242 (pptt) cc_final: 0.7828 (pttp) REVERT: D 70 TYR cc_start: 0.6591 (m-80) cc_final: 0.6387 (m-80) REVERT: E 114 LEU cc_start: 0.2733 (OUTLIER) cc_final: 0.2094 (pp) REVERT: F 114 LEU cc_start: 0.3130 (OUTLIER) cc_final: 0.2561 (pp) REVERT: F 221 ASN cc_start: 0.8351 (m-40) cc_final: 0.8066 (m-40) REVERT: H 45 LYS cc_start: 0.8159 (pptt) cc_final: 0.7584 (pptt) REVERT: H 83 ILE cc_start: 0.8911 (pt) cc_final: 0.8695 (pt) REVERT: H 114 LEU cc_start: 0.2884 (OUTLIER) cc_final: 0.2235 (pp) REVERT: I 85 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8253 (tp) REVERT: I 114 LEU cc_start: 0.3144 (OUTLIER) cc_final: 0.2550 (pp) REVERT: J 70 TYR cc_start: 0.6743 (m-80) cc_final: 0.6483 (m-80) REVERT: K 45 LYS cc_start: 0.8204 (pptt) cc_final: 0.7804 (pptt) REVERT: K 114 LEU cc_start: 0.2784 (OUTLIER) cc_final: 0.2101 (pp) REVERT: L 85 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8318 (tp) REVERT: L 114 LEU cc_start: 0.3182 (OUTLIER) cc_final: 0.2599 (pp) REVERT: L 145 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7800 (mt-10) outliers start: 42 outliers final: 26 residues processed: 336 average time/residue: 0.4929 time to fit residues: 235.8893 Evaluate side-chains 331 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.0470 chunk 253 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 82 GLN C 82 GLN D 82 GLN E 82 GLN F 82 GLN G 82 GLN H 82 GLN I 82 GLN K 82 GLN L 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113781 restraints weight = 34313.453| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.20 r_work: 0.3061 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 552 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26052 Z= 0.192 Angle : 0.479 7.648 35232 Z= 0.251 Chirality : 0.042 0.147 3684 Planarity : 0.003 0.029 4536 Dihedral : 3.740 18.934 3432 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.48 % Allowed : 12.04 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3036 helix: 1.34 (0.15), residues: 1296 sheet: -2.15 (0.46), residues: 144 loop : -0.89 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 22 HIS 0.002 0.001 HIS D 57 PHE 0.012 0.001 PHE I 64 TYR 0.015 0.001 TYR H 92 ARG 0.005 0.000 ARG F 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6104.54 seconds wall clock time: 111 minutes 33.78 seconds (6693.78 seconds total)