Starting phenix.real_space_refine on Mon Mar 18 16:48:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/03_2024/7x6l_33023.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/03_2024/7x6l_33023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/03_2024/7x6l_33023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/03_2024/7x6l_33023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/03_2024/7x6l_33023.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/03_2024/7x6l_33023.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 102 5.16 5 C 13422 2.51 5 N 3705 2.21 5 O 4257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21486 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "K" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "J" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "D" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 12.75, per 1000 atoms: 0.59 Number of scatterers: 21486 At special positions: 0 Unit cell: (175.294, 175.294, 142.344, 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 102 16.00 O 4257 8.00 N 3705 7.00 C 13422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 102 " - pdb=" SG CYS I 107 " distance=2.03 Simple disulfide: pdb=" SG CYS I 157 " - pdb=" SG CYS I 213 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS G 157 " - pdb=" SG CYS G 213 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 3.6 seconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 63 sheets defined 15.1% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'I' and resid 204 through 206 No H-bonds generated for 'chain 'I' and resid 204 through 206' Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.600A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 189 removed outlier: 3.710A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.505A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.987A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.578A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 109 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.690A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 54 removed outlier: 4.041A pdb=" N GLN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.791A pdb=" N GLU B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.610A pdb=" N ALA B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'J' and resid 121 through 126 removed outlier: 3.511A pdb=" N LEU J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 121 through 126' Processing helix chain 'J' and resid 183 through 189 removed outlier: 3.722A pdb=" N GLU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS J 189 " --> pdb=" O ASP J 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.985A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.615A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 109 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.692A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 54 removed outlier: 4.043A pdb=" N GLN E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 124 removed outlier: 3.650A pdb=" N GLU E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 154 removed outlier: 3.501A pdb=" N ILE E 152 " --> pdb=" O CYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.624A pdb=" N ALA E 166 " --> pdb=" O TYR E 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.515A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 121 through 126' Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.709A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.984A pdb=" N ASP D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL D 78 " --> pdb=" O HIS D 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN D 80 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.653A pdb=" N LEU D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 109 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.684A pdb=" N GLN D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 54 removed outlier: 4.012A pdb=" N GLN F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 51 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 124 removed outlier: 3.760A pdb=" N GLU F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 162 through 171 removed outlier: 3.612A pdb=" N ALA F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.518A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS I 22 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.678A pdb=" N THR I 124 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR I 94 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL I 126 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA I 92 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 97 through 98 removed outlier: 3.899A pdb=" N VAL I 119 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.999A pdb=" N VAL I 201 " --> pdb=" O ALA I 153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU I 155 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.999A pdb=" N VAL I 201 " --> pdb=" O ALA I 153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU I 155 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 168 through 171 removed outlier: 3.678A pdb=" N THR I 168 " --> pdb=" O ASN I 216 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN I 216 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR I 211 " --> pdb=" O VAL I 228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS I 226 " --> pdb=" O CYS I 213 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL I 215 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR I 222 " --> pdb=" O HIS I 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 7 removed outlier: 3.961A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.209A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.747A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA K 130 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL K 132 " --> pdb=" O LEU K 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 145 through 150 removed outlier: 3.783A pdb=" N LYS K 149 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.546A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 25 " --> pdb=" O CYS A 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 14 " --> pdb=" O ARG B 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.825A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 34 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.583A pdb=" N GLN A 44 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.726A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 58 through 61 removed outlier: 5.692A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 136 through 141 removed outlier: 5.197A pdb=" N CYS A 139 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.735A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 235 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 180 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 229 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.735A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.646A pdb=" N LEU A 164 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 166 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 245 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.579A pdb=" N ILE A 282 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 302 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.517A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS G 22 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLY G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G 124 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR G 94 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 126 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 92 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 97 through 98 removed outlier: 3.915A pdb=" N VAL G 119 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 137 through 140 removed outlier: 4.015A pdb=" N VAL G 201 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU G 155 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 197 " --> pdb=" O CYS G 157 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 161 " --> pdb=" O TYR G 193 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR G 193 " --> pdb=" O ASP G 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 198 " --> pdb=" O HIS G 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 137 through 140 removed outlier: 4.015A pdb=" N VAL G 201 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU G 155 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 197 " --> pdb=" O CYS G 157 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 161 " --> pdb=" O TYR G 193 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR G 193 " --> pdb=" O ASP G 161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 168 through 171 removed outlier: 3.662A pdb=" N THR G 168 " --> pdb=" O ASN G 216 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN G 216 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR G 211 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 226 " --> pdb=" O CYS G 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 215 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR G 222 " --> pdb=" O HIS G 217 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 6 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.228A pdb=" N VAL J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 114 through 118 removed outlier: 3.714A pdb=" N ASN J 137 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL J 133 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 130 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL J 132 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 145 through 150 removed outlier: 3.799A pdb=" N LYS J 149 " --> pdb=" O ALA J 193 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR J 192 " --> pdb=" O PHE J 209 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS J 207 " --> pdb=" O CYS J 194 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 31 through 35 removed outlier: 3.545A pdb=" N GLY E 33 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY E 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 16 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 25 " --> pdb=" O CYS C 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS C 14 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.832A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 34 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD8, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.544A pdb=" N GLN C 44 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.712A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 58 through 61 removed outlier: 5.706A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 136 through 141 removed outlier: 5.217A pdb=" N CYS C 139 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 144 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.755A pdb=" N GLY C 181 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 235 " --> pdb=" O TYR C 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP C 180 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 229 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.755A pdb=" N GLY C 181 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.691A pdb=" N VAL C 166 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 245 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.656A pdb=" N ILE C 282 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 302 " --> pdb=" O ILE C 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.521A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.685A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 92 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 97 through 98 removed outlier: 3.923A pdb=" N VAL H 119 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 137 through 140 removed outlier: 4.012A pdb=" N VAL H 201 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU H 155 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 197 " --> pdb=" O CYS H 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP H 161 " --> pdb=" O TYR H 193 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 137 through 140 removed outlier: 4.012A pdb=" N VAL H 201 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU H 155 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 197 " --> pdb=" O CYS H 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP H 161 " --> pdb=" O TYR H 193 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 168 through 171 removed outlier: 3.689A pdb=" N THR H 168 " --> pdb=" O ASN H 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN H 216 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR H 211 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS H 226 " --> pdb=" O CYS H 213 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 215 " --> pdb=" O VAL H 224 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR H 222 " --> pdb=" O HIS H 217 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.886A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.218A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.708A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.790A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 31 through 35 removed outlier: 3.589A pdb=" N GLY F 33 " --> pdb=" O HIS F 26 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY F 23 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 25 " --> pdb=" O CYS D 14 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS D 14 " --> pdb=" O ARG F 25 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.832A pdb=" N THR D 24 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 34 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AG2, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.564A pdb=" N GLN D 44 " --> pdb=" O PHE D 294 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 51 through 54 removed outlier: 5.710A pdb=" N ILE D 51 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS D 277 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN D 53 " --> pdb=" O CYS D 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 58 through 61 removed outlier: 5.700A pdb=" N PHE D 87 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 136 through 141 removed outlier: 5.177A pdb=" N CYS D 139 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY D 144 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.788A pdb=" N GLY D 181 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 235 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP D 180 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 229 " --> pdb=" O HIS D 184 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.788A pdb=" N GLY D 181 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.693A pdb=" N VAL D 166 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 245 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 281 through 282 removed outlier: 3.553A pdb=" N ILE D 282 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 302 " --> pdb=" O ILE D 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 653 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3618 1.32 - 1.44: 6018 1.44 - 1.57: 12174 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 21945 Sorted by residual: bond pdb=" C PRO A 324 " pdb=" O PRO A 324 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 1.469 1.442 0.026 1.28e-02 6.10e+03 4.19e+00 bond pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 1.520 1.498 0.021 1.42e-02 4.96e+03 2.26e+00 bond pdb=" C LYS H 218 " pdb=" N PRO H 219 " ideal model delta sigma weight residual 1.337 1.352 -0.016 1.06e-02 8.90e+03 2.23e+00 bond pdb=" CA PRO A 324 " pdb=" CB PRO A 324 " ideal model delta sigma weight residual 1.533 1.513 0.020 1.42e-02 4.96e+03 2.05e+00 ... (remaining 21940 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.73: 474 105.73 - 112.79: 11742 112.79 - 119.85: 6865 119.85 - 126.91: 10416 126.91 - 133.98: 293 Bond angle restraints: 29790 Sorted by residual: angle pdb=" C SER J 67 " pdb=" CA SER J 67 " pdb=" CB SER J 67 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.46e+00 4.69e-01 1.97e+01 angle pdb=" C PRO A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C VAL A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 119.84 116.15 3.69 1.25e+00 6.40e-01 8.70e+00 angle pdb=" CA SER J 67 " pdb=" C SER J 67 " pdb=" N GLY J 68 " ideal model delta sigma weight residual 118.57 116.17 2.40 8.80e-01 1.29e+00 7.41e+00 angle pdb=" CA LYS H 218 " pdb=" C LYS H 218 " pdb=" N PRO H 219 " ideal model delta sigma weight residual 118.44 122.36 -3.92 1.59e+00 3.96e-01 6.08e+00 ... (remaining 29785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 12808 17.48 - 34.96: 305 34.96 - 52.44: 41 52.44 - 69.93: 7 69.93 - 87.41: 3 Dihedral angle restraints: 13164 sinusoidal: 5175 harmonic: 7989 Sorted by residual: dihedral pdb=" CA PRO A 324 " pdb=" C PRO A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" N CYS D 76 " pdb=" CA CYS D 76 " pdb=" CB CYS D 76 " pdb=" SG CYS D 76 " ideal model delta sinusoidal sigma weight residual 60.00 1.20 58.80 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N CYS A 76 " pdb=" CA CYS A 76 " pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " ideal model delta sinusoidal sigma weight residual 60.00 1.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 13161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2701 0.048 - 0.096: 394 0.096 - 0.144: 210 0.144 - 0.191: 3 0.191 - 0.239: 1 Chirality restraints: 3309 Sorted by residual: chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LYS G 218 " pdb=" N LYS G 218 " pdb=" C LYS G 218 " pdb=" CB LYS G 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA LYS I 218 " pdb=" N LYS I 218 " pdb=" C LYS I 218 " pdb=" CB LYS I 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 3306 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 323 " 0.086 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO A 324 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 323 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL A 323 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 323 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO A 324 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 238 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 239 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " -0.021 5.00e-02 4.00e+02 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6063 2.81 - 3.33: 15982 3.33 - 3.86: 36058 3.86 - 4.38: 39232 4.38 - 4.90: 69614 Nonbonded interactions: 166949 Sorted by model distance: nonbonded pdb=" OG1 THR A 283 " pdb=" O GLY A 286 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR D 283 " pdb=" O GLY D 286 " model vdw 2.292 2.440 nonbonded pdb=" OG1 THR C 283 " pdb=" O GLY C 286 " model vdw 2.294 2.440 nonbonded pdb=" O GLU E 103 " pdb=" OG1 THR E 107 " model vdw 2.309 2.440 nonbonded pdb=" O GLU B 103 " pdb=" OG1 THR B 107 " model vdw 2.310 2.440 ... (remaining 166944 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 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.640 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 54.920 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.140 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 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 : 0.002 0.041 21945 Z= 0.131 Angle : 0.447 7.459 29790 Z= 0.262 Chirality : 0.041 0.239 3309 Planarity : 0.005 0.133 3876 Dihedral : 7.433 87.406 7953 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.92 % Favored : 97.89 % Rotamer: Outliers : 2.04 % Allowed : 2.37 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % 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: -3.07 (0.13), residues: 2754 helix: -4.45 (0.08), residues: 303 sheet: -1.05 (0.17), residues: 807 loop : -2.13 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 180 HIS 0.002 0.000 HIS I 217 PHE 0.008 0.001 PHE B 63 TYR 0.007 0.001 TYR L 49 ARG 0.001 0.000 ARG F 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 694 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 77 ASN cc_start: 0.5182 (m-40) cc_final: 0.4659 (p0) REVERT: I 115 TYR cc_start: 0.5421 (m-80) cc_final: 0.5185 (m-80) REVERT: I 161 ASP cc_start: 0.8056 (m-30) cc_final: 0.7814 (p0) REVERT: I 181 HIS cc_start: 0.6415 (m-70) cc_final: 0.5943 (m-70) REVERT: I 195 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6767 (pp) REVERT: I 212 ILE cc_start: 0.6421 (mt) cc_final: 0.6011 (tp) REVERT: K 82 ASP cc_start: 0.6856 (m-30) cc_final: 0.6268 (t0) REVERT: K 139 PHE cc_start: 0.4856 (p90) cc_final: 0.4613 (p90) REVERT: K 172 THR cc_start: 0.8220 (p) cc_final: 0.7973 (m) REVERT: K 210 ASN cc_start: 0.7934 (t0) cc_final: 0.7696 (p0) REVERT: A 75 HIS cc_start: 0.7027 (m-70) cc_final: 0.6588 (m-70) REVERT: A 119 GLU cc_start: 0.7073 (tt0) cc_final: 0.6358 (tt0) REVERT: A 121 ILE cc_start: 0.8385 (mp) cc_final: 0.8157 (mm) REVERT: A 177 LEU cc_start: 0.6891 (tp) cc_final: 0.5996 (mp) REVERT: A 208 ARG cc_start: 0.7141 (mtt90) cc_final: 0.6846 (mtt90) REVERT: A 223 VAL cc_start: 0.7540 (t) cc_final: 0.7155 (p) REVERT: B 25 ARG cc_start: 0.7102 (tmt170) cc_final: 0.6882 (tmt170) REVERT: B 79 ASP cc_start: 0.6202 (m-30) cc_final: 0.5957 (m-30) REVERT: B 85 GLU cc_start: 0.7158 (tp30) cc_final: 0.6613 (tp30) REVERT: B 89 ILE cc_start: 0.8148 (mt) cc_final: 0.7797 (mt) REVERT: B 94 TYR cc_start: 0.7567 (t80) cc_final: 0.7219 (t80) REVERT: B 121 LYS cc_start: 0.7949 (ttpt) cc_final: 0.7616 (tptp) REVERT: G 77 ASN cc_start: 0.4696 (m-40) cc_final: 0.4434 (p0) REVERT: G 115 TYR cc_start: 0.4746 (m-80) cc_final: 0.4395 (m-10) REVERT: G 171 TRP cc_start: 0.6104 (m100) cc_final: 0.5807 (m100) REVERT: J 62 PHE cc_start: 0.6179 (m-80) cc_final: 0.5964 (m-80) REVERT: J 95 PRO cc_start: 0.7596 (Cg_endo) cc_final: 0.7105 (Cg_exo) REVERT: J 139 PHE cc_start: 0.5019 (p90) cc_final: 0.4530 (p90) REVERT: J 172 THR cc_start: 0.8308 (p) cc_final: 0.8067 (m) REVERT: C 40 THR cc_start: 0.8276 (t) cc_final: 0.8004 (p) REVERT: C 50 LYS cc_start: 0.7092 (mttt) cc_final: 0.6758 (mttt) REVERT: C 60 ASP cc_start: 0.7753 (t0) cc_final: 0.7378 (t0) REVERT: C 75 HIS cc_start: 0.6902 (m-70) cc_final: 0.6546 (m-70) REVERT: C 83 THR cc_start: 0.7836 (p) cc_final: 0.6802 (p) REVERT: C 92 LYS cc_start: 0.8391 (pttp) cc_final: 0.8164 (pttp) REVERT: C 117 THR cc_start: 0.8670 (t) cc_final: 0.8012 (m) REVERT: C 119 GLU cc_start: 0.7206 (tt0) cc_final: 0.6528 (tt0) REVERT: C 121 ILE cc_start: 0.8807 (mp) cc_final: 0.8422 (mm) REVERT: C 182 VAL cc_start: 0.5160 (t) cc_final: 0.4437 (t) REVERT: C 184 HIS cc_start: 0.6233 (m-70) cc_final: 0.5989 (m-70) REVERT: C 208 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6576 (mtt90) REVERT: C 213 ILE cc_start: 0.8319 (mm) cc_final: 0.8090 (mm) REVERT: C 223 VAL cc_start: 0.7528 (t) cc_final: 0.7201 (p) REVERT: C 245 ILE cc_start: 0.8808 (mt) cc_final: 0.8553 (mp) REVERT: C 261 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6803 (mtt180) REVERT: C 268 MET cc_start: 0.7864 (ttm) cc_final: 0.7648 (ttm) REVERT: C 275 ASP cc_start: 0.7304 (t0) cc_final: 0.7067 (t0) REVERT: C 307 LYS cc_start: 0.5150 (mttp) cc_final: 0.4786 (mttp) REVERT: E 25 ARG cc_start: 0.6886 (tmt170) cc_final: 0.6653 (tmt170) REVERT: E 49 ASN cc_start: 0.6907 (t0) cc_final: 0.6666 (t0) REVERT: E 79 ASP cc_start: 0.5941 (m-30) cc_final: 0.5669 (m-30) REVERT: E 81 GLU cc_start: 0.6610 (pt0) cc_final: 0.6227 (pt0) REVERT: E 85 GLU cc_start: 0.6806 (tp30) cc_final: 0.6473 (tp30) REVERT: E 90 ASP cc_start: 0.6783 (m-30) cc_final: 0.6523 (m-30) REVERT: E 91 LEU cc_start: 0.8012 (mt) cc_final: 0.7471 (mt) REVERT: E 95 ASN cc_start: 0.7771 (m-40) cc_final: 0.7422 (m-40) REVERT: E 102 LEU cc_start: 0.7695 (tp) cc_final: 0.7433 (tp) REVERT: E 114 GLU cc_start: 0.6419 (mm-30) cc_final: 0.5795 (mm-30) REVERT: H 12 VAL cc_start: 0.8199 (OUTLIER) cc_final: 0.7994 (t) REVERT: H 29 PHE cc_start: 0.7497 (t80) cc_final: 0.6502 (t80) REVERT: H 126 VAL cc_start: 0.6339 (t) cc_final: 0.5974 (p) REVERT: H 195 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6511 (pp) REVERT: L 18 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6949 (ttm170) REVERT: L 73 LEU cc_start: 0.6923 (tp) cc_final: 0.6699 (tp) REVERT: L 139 PHE cc_start: 0.5220 (p90) cc_final: 0.4939 (p90) REVERT: L 180 THR cc_start: 0.7554 (m) cc_final: 0.7322 (t) REVERT: L 210 ASN cc_start: 0.7508 (t0) cc_final: 0.7161 (p0) REVERT: D 50 LYS cc_start: 0.7197 (mttt) cc_final: 0.6636 (mtmm) REVERT: D 53 ASN cc_start: 0.6638 (p0) cc_final: 0.6384 (t0) REVERT: D 57 ARG cc_start: 0.7519 (ttt90) cc_final: 0.6416 (ttt90) REVERT: D 60 ASP cc_start: 0.7428 (t0) cc_final: 0.7192 (t0) REVERT: D 74 PRO cc_start: 0.7171 (Cg_exo) cc_final: 0.6292 (Cg_endo) REVERT: D 75 HIS cc_start: 0.7133 (m-70) cc_final: 0.6851 (m-70) REVERT: D 77 ASP cc_start: 0.7573 (m-30) cc_final: 0.7085 (m-30) REVERT: D 83 THR cc_start: 0.7463 (p) cc_final: 0.5561 (t) REVERT: D 121 ILE cc_start: 0.8784 (mp) cc_final: 0.8509 (mm) REVERT: D 152 ASN cc_start: 0.4798 (t0) cc_final: 0.3965 (t0) REVERT: D 164 LEU cc_start: 0.6987 (mt) cc_final: 0.6748 (pp) REVERT: D 182 VAL cc_start: 0.5072 (t) cc_final: 0.4859 (m) REVERT: D 184 HIS cc_start: 0.6148 (m-70) cc_final: 0.5808 (m-70) REVERT: D 186 SER cc_start: 0.7695 (p) cc_final: 0.7388 (m) REVERT: D 207 ARG cc_start: 0.6404 (mtt180) cc_final: 0.5936 (mmm-85) REVERT: F 79 ASP cc_start: 0.6171 (m-30) cc_final: 0.5915 (m-30) REVERT: F 85 GLU cc_start: 0.6816 (tp30) cc_final: 0.6051 (tp30) REVERT: F 89 ILE cc_start: 0.7915 (mt) cc_final: 0.7485 (mt) REVERT: F 91 LEU cc_start: 0.7966 (mt) cc_final: 0.7622 (mt) REVERT: F 94 TYR cc_start: 0.8044 (t80) cc_final: 0.7789 (t80) outliers start: 49 outliers final: 14 residues processed: 730 average time/residue: 0.3418 time to fit residues: 374.2532 Evaluate side-chains 588 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 571 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 56 ASN I 106 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN K 90 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN A 44 GLN A 53 ASN A 56 HIS A 250 ASN A 290 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 106 ASN ** G 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN C 250 ASN C 285 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS E 168 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 106 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 160 GLN D 44 GLN D 285 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 21945 Z= 0.259 Angle : 0.636 11.056 29790 Z= 0.330 Chirality : 0.045 0.184 3309 Planarity : 0.005 0.071 3876 Dihedral : 4.373 54.908 3019 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.36 % Favored : 97.53 % Rotamer: Outliers : 2.74 % Allowed : 8.23 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % 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: -2.07 (0.15), residues: 2754 helix: -1.84 (0.22), residues: 351 sheet: -0.71 (0.18), residues: 801 loop : -1.64 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 148 HIS 0.010 0.002 HIS F 106 PHE 0.030 0.002 PHE I 29 TYR 0.023 0.002 TYR B 141 ARG 0.005 0.001 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 617 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 22 CYS cc_start: 0.5437 (t) cc_final: 0.4983 (t) REVERT: I 79 LEU cc_start: 0.7822 (mt) cc_final: 0.7612 (mm) REVERT: I 83 MET cc_start: 0.5422 (mtp) cc_final: 0.4795 (mtp) REVERT: I 110 VAL cc_start: 0.7979 (t) cc_final: 0.7740 (m) REVERT: I 115 TYR cc_start: 0.6019 (m-80) cc_final: 0.5756 (m-80) REVERT: I 117 MET cc_start: 0.6876 (mtm) cc_final: 0.6221 (mtt) REVERT: I 181 HIS cc_start: 0.6106 (m-70) cc_final: 0.5458 (m-70) REVERT: K 62 PHE cc_start: 0.7226 (t80) cc_final: 0.6979 (t80) REVERT: K 139 PHE cc_start: 0.4969 (p90) cc_final: 0.4309 (p90) REVERT: K 147 GLN cc_start: 0.6232 (pp30) cc_final: 0.5795 (pp30) REVERT: K 172 THR cc_start: 0.8290 (p) cc_final: 0.8067 (m) REVERT: K 176 SER cc_start: 0.7397 (t) cc_final: 0.7016 (p) REVERT: K 177 SER cc_start: 0.7034 (t) cc_final: 0.6334 (p) REVERT: K 210 ASN cc_start: 0.8366 (t0) cc_final: 0.7988 (p0) REVERT: A 57 ARG cc_start: 0.7677 (ttt90) cc_final: 0.6780 (ttt90) REVERT: A 75 HIS cc_start: 0.7264 (m-70) cc_final: 0.6714 (m-70) REVERT: A 119 GLU cc_start: 0.7469 (tt0) cc_final: 0.6645 (tt0) REVERT: A 121 ILE cc_start: 0.8377 (mp) cc_final: 0.8131 (mm) REVERT: A 123 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5806 (mm-30) REVERT: A 223 VAL cc_start: 0.7480 (t) cc_final: 0.7088 (p) REVERT: A 257 TYR cc_start: 0.6842 (p90) cc_final: 0.6616 (p90) REVERT: A 275 ASP cc_start: 0.7133 (t0) cc_final: 0.6909 (t0) REVERT: B 79 ASP cc_start: 0.7089 (m-30) cc_final: 0.6798 (m-30) REVERT: B 85 GLU cc_start: 0.7475 (tp30) cc_final: 0.6934 (tp30) REVERT: B 89 ILE cc_start: 0.8314 (mt) cc_final: 0.7925 (mt) REVERT: B 91 LEU cc_start: 0.7705 (mt) cc_final: 0.7468 (mt) REVERT: B 94 TYR cc_start: 0.8046 (t80) cc_final: 0.7515 (t80) REVERT: B 95 ASN cc_start: 0.7707 (m-40) cc_final: 0.7473 (m-40) REVERT: B 121 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7756 (tptp) REVERT: B 133 MET cc_start: 0.5530 (ptm) cc_final: 0.5257 (ptm) REVERT: G 3 GLN cc_start: 0.6274 (mp10) cc_final: 0.6031 (mp10) REVERT: G 20 LEU cc_start: 0.7918 (mt) cc_final: 0.7681 (mt) REVERT: G 46 GLU cc_start: 0.5623 (tp30) cc_final: 0.5417 (tp30) REVERT: G 50 TYR cc_start: 0.5662 (t80) cc_final: 0.5444 (t80) REVERT: G 73 ASP cc_start: 0.7134 (t0) cc_final: 0.6796 (t0) REVERT: G 81 LEU cc_start: 0.4334 (mt) cc_final: 0.3866 (mt) REVERT: G 83 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.5069 (mtp) REVERT: G 94 TYR cc_start: 0.3611 (m-80) cc_final: 0.3176 (m-80) REVERT: J 27 GLN cc_start: 0.6919 (pp30) cc_final: 0.6651 (pp30) REVERT: J 29 ILE cc_start: 0.7486 (pt) cc_final: 0.7218 (tt) REVERT: J 62 PHE cc_start: 0.6353 (m-80) cc_final: 0.5975 (m-80) REVERT: J 74 THR cc_start: 0.6843 (m) cc_final: 0.6250 (m) REVERT: J 139 PHE cc_start: 0.5003 (p90) cc_final: 0.4498 (p90) REVERT: J 172 THR cc_start: 0.8285 (p) cc_final: 0.8040 (m) REVERT: J 179 LEU cc_start: 0.7627 (tp) cc_final: 0.7368 (mt) REVERT: J 189 HIS cc_start: 0.7722 (m-70) cc_final: 0.7438 (m-70) REVERT: C 50 LYS cc_start: 0.7444 (mttt) cc_final: 0.6818 (mtmm) REVERT: C 92 LYS cc_start: 0.8484 (pttp) cc_final: 0.8164 (pttp) REVERT: C 100 TYR cc_start: 0.7261 (p90) cc_final: 0.7057 (p90) REVERT: C 109 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7343 (mtp-110) REVERT: C 119 GLU cc_start: 0.7504 (tt0) cc_final: 0.6758 (tt0) REVERT: C 121 ILE cc_start: 0.8737 (mp) cc_final: 0.8451 (mm) REVERT: C 123 GLU cc_start: 0.4897 (mt-10) cc_final: 0.4588 (mt-10) REVERT: C 161 TYR cc_start: 0.6552 (t80) cc_final: 0.6082 (t80) REVERT: C 167 THR cc_start: 0.7784 (m) cc_final: 0.7322 (t) REVERT: C 184 HIS cc_start: 0.6351 (m-70) cc_final: 0.6064 (m-70) REVERT: C 208 ARG cc_start: 0.7156 (mtt90) cc_final: 0.6626 (mtt90) REVERT: C 245 ILE cc_start: 0.8433 (mt) cc_final: 0.8209 (mp) REVERT: C 260 MET cc_start: 0.7025 (mmm) cc_final: 0.6767 (mmp) REVERT: C 269 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.7422 (mtt90) REVERT: C 275 ASP cc_start: 0.7208 (t0) cc_final: 0.6998 (t0) REVERT: E 78 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6548 (mp10) REVERT: E 79 ASP cc_start: 0.7059 (m-30) cc_final: 0.6847 (m-30) REVERT: E 81 GLU cc_start: 0.7124 (pt0) cc_final: 0.6733 (pt0) REVERT: E 85 GLU cc_start: 0.6981 (tp30) cc_final: 0.6759 (tp30) REVERT: E 91 LEU cc_start: 0.8208 (mt) cc_final: 0.7630 (mt) REVERT: E 95 ASN cc_start: 0.8109 (m-40) cc_final: 0.7720 (m-40) REVERT: E 102 LEU cc_start: 0.7857 (tp) cc_final: 0.7552 (tp) REVERT: E 133 MET cc_start: 0.5738 (ptp) cc_final: 0.5514 (ptm) REVERT: H 29 PHE cc_start: 0.7265 (t80) cc_final: 0.6988 (t80) REVERT: H 117 MET cc_start: 0.7076 (mtm) cc_final: 0.6382 (mpp) REVERT: H 181 HIS cc_start: 0.6114 (m-70) cc_final: 0.5795 (m-70) REVERT: L 18 ARG cc_start: 0.7393 (ttm170) cc_final: 0.7171 (ttm170) REVERT: L 29 ILE cc_start: 0.7288 (pt) cc_final: 0.7047 (tt) REVERT: L 139 PHE cc_start: 0.5164 (p90) cc_final: 0.4829 (p90) REVERT: L 180 THR cc_start: 0.7319 (m) cc_final: 0.7090 (t) REVERT: L 210 ASN cc_start: 0.7848 (t0) cc_final: 0.7591 (p0) REVERT: D 75 HIS cc_start: 0.6913 (m-70) cc_final: 0.6569 (m-70) REVERT: D 83 THR cc_start: 0.7539 (p) cc_final: 0.7256 (t) REVERT: D 119 GLU cc_start: 0.7586 (tt0) cc_final: 0.7291 (tt0) REVERT: D 123 GLU cc_start: 0.5667 (mt-10) cc_final: 0.5326 (mt-10) REVERT: D 127 TRP cc_start: 0.7884 (m-90) cc_final: 0.6565 (m-90) REVERT: D 150 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7592 (mmm160) REVERT: D 184 HIS cc_start: 0.6350 (m-70) cc_final: 0.5958 (m-70) REVERT: D 186 SER cc_start: 0.8002 (p) cc_final: 0.7681 (m) REVERT: D 212 THR cc_start: 0.8348 (m) cc_final: 0.8086 (p) REVERT: D 224 ARG cc_start: 0.7680 (mpt180) cc_final: 0.7409 (mpt-90) REVERT: D 326 LYS cc_start: 0.7819 (ptmm) cc_final: 0.6816 (ptpp) REVERT: F 41 THR cc_start: 0.7408 (m) cc_final: 0.7081 (m) REVERT: F 79 ASP cc_start: 0.6871 (m-30) cc_final: 0.6549 (m-30) REVERT: F 85 GLU cc_start: 0.6854 (tp30) cc_final: 0.6519 (tp30) REVERT: F 87 THR cc_start: 0.7697 (t) cc_final: 0.7363 (p) REVERT: F 89 ILE cc_start: 0.7945 (mt) cc_final: 0.7466 (mt) REVERT: F 91 LEU cc_start: 0.7826 (mt) cc_final: 0.7572 (mt) REVERT: F 114 GLU cc_start: 0.6571 (mm-30) cc_final: 0.5977 (mm-30) REVERT: F 115 MET cc_start: 0.5780 (tpp) cc_final: 0.5535 (tpp) REVERT: F 121 LYS cc_start: 0.8076 (tptp) cc_final: 0.7801 (tptp) REVERT: F 133 MET cc_start: 0.5467 (ptm) cc_final: 0.5119 (ptm) outliers start: 66 outliers final: 44 residues processed: 647 average time/residue: 0.3450 time to fit residues: 333.4016 Evaluate side-chains 621 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 575 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 291 ASP Chi-restraints excluded: chain F residue 25 ARG Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN A 250 ASN A 290 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 GLN C 250 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 166 GLN D 56 HIS ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.133 21945 Z= 0.439 Angle : 0.789 14.509 29790 Z= 0.423 Chirality : 0.049 0.321 3309 Planarity : 0.006 0.064 3876 Dihedral : 5.538 59.650 3010 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 4.82 % Allowed : 9.85 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % 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: -1.96 (0.15), residues: 2754 helix: -0.95 (0.24), residues: 375 sheet: -0.85 (0.17), residues: 861 loop : -1.66 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP H 36 HIS 0.016 0.002 HIS L 87 PHE 0.034 0.003 PHE E 171 TYR 0.039 0.003 TYR E 141 ARG 0.012 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 620 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: I 3 GLN cc_start: 0.6212 (mp-120) cc_final: 0.5859 (mm-40) REVERT: I 22 CYS cc_start: 0.5374 (t) cc_final: 0.4941 (t) REVERT: I 68 PHE cc_start: 0.7707 (m-80) cc_final: 0.7360 (m-80) REVERT: I 83 MET cc_start: 0.5770 (mtp) cc_final: 0.4549 (mtp) REVERT: I 104 SER cc_start: 0.8199 (t) cc_final: 0.7986 (t) REVERT: I 110 VAL cc_start: 0.8146 (t) cc_final: 0.7886 (m) REVERT: I 117 MET cc_start: 0.6849 (mtm) cc_final: 0.6286 (mtt) REVERT: I 181 HIS cc_start: 0.5463 (m-70) cc_final: 0.5009 (m-70) REVERT: K 62 PHE cc_start: 0.7465 (t80) cc_final: 0.7248 (t80) REVERT: K 73 LEU cc_start: 0.7688 (tp) cc_final: 0.7441 (tp) REVERT: K 147 GLN cc_start: 0.6459 (pp30) cc_final: 0.5167 (mp10) REVERT: K 189 HIS cc_start: 0.7757 (m-70) cc_final: 0.7474 (m-70) REVERT: K 210 ASN cc_start: 0.8477 (t0) cc_final: 0.8066 (p0) REVERT: A 57 ARG cc_start: 0.7666 (ttt90) cc_final: 0.6888 (ttt90) REVERT: A 75 HIS cc_start: 0.6786 (m-70) cc_final: 0.6172 (m-70) REVERT: A 119 GLU cc_start: 0.7449 (tt0) cc_final: 0.6527 (tt0) REVERT: A 121 ILE cc_start: 0.8209 (mp) cc_final: 0.7865 (mm) REVERT: A 123 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6266 (mm-30) REVERT: A 184 HIS cc_start: 0.6967 (m-70) cc_final: 0.6035 (m170) REVERT: A 208 ARG cc_start: 0.7302 (mtt90) cc_final: 0.6930 (mtt90) REVERT: A 261 ARG cc_start: 0.7572 (mtt90) cc_final: 0.7360 (mmt90) REVERT: A 275 ASP cc_start: 0.7047 (t0) cc_final: 0.6805 (t0) REVERT: B 25 ARG cc_start: 0.6963 (tmt170) cc_final: 0.6376 (tmt170) REVERT: B 79 ASP cc_start: 0.7189 (m-30) cc_final: 0.6940 (m-30) REVERT: B 91 LEU cc_start: 0.7579 (mt) cc_final: 0.7306 (mt) REVERT: B 94 TYR cc_start: 0.8390 (t80) cc_final: 0.7738 (t80) REVERT: B 95 ASN cc_start: 0.7893 (m-40) cc_final: 0.7659 (m-40) REVERT: B 115 MET cc_start: 0.6155 (tpp) cc_final: 0.5848 (tpp) REVERT: B 121 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7626 (tptp) REVERT: B 133 MET cc_start: 0.5692 (ptm) cc_final: 0.5274 (ptm) REVERT: G 3 GLN cc_start: 0.6575 (mp10) cc_final: 0.6076 (mp10) REVERT: G 51 ILE cc_start: 0.7214 (tp) cc_final: 0.6741 (mm) REVERT: G 68 PHE cc_start: 0.7411 (m-80) cc_final: 0.7067 (m-80) REVERT: G 83 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.4457 (mtp) REVERT: J 5 THR cc_start: 0.7155 (OUTLIER) cc_final: 0.6861 (t) REVERT: J 18 ARG cc_start: 0.7430 (ttm170) cc_final: 0.7180 (ttm170) REVERT: J 29 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7627 (pt) REVERT: J 89 GLN cc_start: 0.6815 (pp30) cc_final: 0.6483 (pp30) REVERT: J 139 PHE cc_start: 0.5058 (p90) cc_final: 0.4627 (p90) REVERT: J 172 THR cc_start: 0.8403 (p) cc_final: 0.8189 (m) REVERT: C 40 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8049 (p) REVERT: C 50 LYS cc_start: 0.7412 (mttt) cc_final: 0.6758 (mtmm) REVERT: C 92 LYS cc_start: 0.8381 (pttp) cc_final: 0.7955 (pttp) REVERT: C 119 GLU cc_start: 0.7385 (tt0) cc_final: 0.7177 (tt0) REVERT: C 123 GLU cc_start: 0.6263 (mt-10) cc_final: 0.6002 (mt-10) REVERT: C 153 TRP cc_start: 0.7050 (t60) cc_final: 0.6756 (t-100) REVERT: C 167 THR cc_start: 0.8174 (m) cc_final: 0.7844 (t) REVERT: C 184 HIS cc_start: 0.6859 (m-70) cc_final: 0.6139 (m170) REVERT: C 208 ARG cc_start: 0.7148 (mtt90) cc_final: 0.6576 (mtt90) REVERT: C 269 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7428 (mtt-85) REVERT: C 290 ASN cc_start: 0.6787 (p0) cc_final: 0.6465 (m110) REVERT: E 25 ARG cc_start: 0.7171 (tmt170) cc_final: 0.6812 (tmt170) REVERT: E 62 LYS cc_start: 0.7539 (tttt) cc_final: 0.6990 (tttt) REVERT: E 78 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: E 79 ASP cc_start: 0.7374 (m-30) cc_final: 0.7031 (m-30) REVERT: E 85 GLU cc_start: 0.7131 (tp30) cc_final: 0.6891 (tp30) REVERT: E 88 LYS cc_start: 0.8448 (tttt) cc_final: 0.7906 (ttmt) REVERT: E 91 LEU cc_start: 0.7786 (mt) cc_final: 0.7135 (mt) REVERT: E 95 ASN cc_start: 0.8024 (m-40) cc_final: 0.7595 (m-40) REVERT: E 102 LEU cc_start: 0.8145 (tp) cc_final: 0.7920 (tp) REVERT: E 110 LEU cc_start: 0.7568 (tp) cc_final: 0.7275 (tt) REVERT: E 114 GLU cc_start: 0.6466 (mm-30) cc_final: 0.5775 (mm-30) REVERT: E 117 LYS cc_start: 0.7993 (mttp) cc_final: 0.7749 (mttp) REVERT: E 133 MET cc_start: 0.6137 (ptp) cc_final: 0.5856 (ptm) REVERT: H 3 GLN cc_start: 0.6241 (mp10) cc_final: 0.5823 (mp10) REVERT: H 20 LEU cc_start: 0.7832 (mt) cc_final: 0.7473 (mt) REVERT: H 65 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8458 (mmmm) REVERT: H 83 MET cc_start: 0.5654 (mtp) cc_final: 0.5380 (mtp) REVERT: H 117 MET cc_start: 0.7525 (mtm) cc_final: 0.6777 (mpp) REVERT: H 126 VAL cc_start: 0.7065 (t) cc_final: 0.6796 (p) REVERT: H 181 HIS cc_start: 0.5949 (m-70) cc_final: 0.5668 (m-70) REVERT: L 4 MET cc_start: 0.5640 (ttm) cc_final: 0.5287 (ttp) REVERT: L 18 ARG cc_start: 0.7497 (ttm170) cc_final: 0.7275 (ttm170) REVERT: L 189 HIS cc_start: 0.8029 (m-70) cc_final: 0.7789 (m-70) REVERT: D 57 ARG cc_start: 0.7802 (ttt90) cc_final: 0.7304 (ttt90) REVERT: D 82 GLU cc_start: 0.7522 (tp30) cc_final: 0.7316 (tp30) REVERT: D 119 GLU cc_start: 0.7625 (tt0) cc_final: 0.7263 (tt0) REVERT: D 123 GLU cc_start: 0.6766 (mt-10) cc_final: 0.5867 (tt0) REVERT: D 141 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7289 (mmt180) REVERT: D 150 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7615 (mmm160) REVERT: D 168 MET cc_start: 0.6401 (mmm) cc_final: 0.5927 (mmm) REVERT: D 184 HIS cc_start: 0.6845 (m-70) cc_final: 0.6316 (m-70) REVERT: D 186 SER cc_start: 0.7816 (p) cc_final: 0.7616 (m) REVERT: D 212 THR cc_start: 0.8482 (m) cc_final: 0.8039 (p) REVERT: D 275 ASP cc_start: 0.7476 (t0) cc_final: 0.7248 (t0) REVERT: F 25 ARG cc_start: 0.6519 (tmt170) cc_final: 0.6227 (tmt170) REVERT: F 79 ASP cc_start: 0.7139 (m-30) cc_final: 0.6796 (m-30) REVERT: F 85 GLU cc_start: 0.6902 (tp30) cc_final: 0.6546 (tp30) REVERT: F 89 ILE cc_start: 0.8162 (mt) cc_final: 0.7594 (mt) REVERT: F 94 TYR cc_start: 0.8720 (t80) cc_final: 0.7713 (t80) REVERT: F 106 HIS cc_start: 0.6680 (t-90) cc_final: 0.6440 (t70) outliers start: 116 outliers final: 81 residues processed: 669 average time/residue: 0.3673 time to fit residues: 374.9563 Evaluate side-chains 673 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 587 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 148 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 233 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 GLN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 33 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 GLN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 21945 Z= 0.399 Angle : 0.740 14.242 29790 Z= 0.392 Chirality : 0.047 0.290 3309 Planarity : 0.005 0.071 3876 Dihedral : 5.667 58.454 3010 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 5.07 % Allowed : 12.64 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.15), residues: 2754 helix: -0.68 (0.25), residues: 375 sheet: -0.83 (0.17), residues: 846 loop : -1.81 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP H 36 HIS 0.011 0.002 HIS K 87 PHE 0.027 0.002 PHE G 29 TYR 0.027 0.003 TYR C 105 ARG 0.009 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 623 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.6187 (mp-120) cc_final: 0.5867 (mm-40) REVERT: I 22 CYS cc_start: 0.5467 (t) cc_final: 0.4964 (t) REVERT: I 68 PHE cc_start: 0.7743 (m-80) cc_final: 0.7085 (m-80) REVERT: I 83 MET cc_start: 0.5757 (mtp) cc_final: 0.4145 (mtp) REVERT: I 117 MET cc_start: 0.6812 (mtm) cc_final: 0.6296 (mtt) REVERT: I 181 HIS cc_start: 0.5502 (m-70) cc_final: 0.5045 (m-70) REVERT: K 62 PHE cc_start: 0.7288 (t80) cc_final: 0.7038 (t80) REVERT: K 100 GLN cc_start: 0.6744 (mt0) cc_final: 0.6453 (mp10) REVERT: K 177 SER cc_start: 0.7431 (t) cc_final: 0.7055 (t) REVERT: K 210 ASN cc_start: 0.8440 (t0) cc_final: 0.8089 (p0) REVERT: A 57 ARG cc_start: 0.7533 (ttt90) cc_final: 0.6755 (ttm-80) REVERT: A 75 HIS cc_start: 0.6788 (m-70) cc_final: 0.6257 (m-70) REVERT: A 82 GLU cc_start: 0.7663 (tp30) cc_final: 0.7272 (tp30) REVERT: A 119 GLU cc_start: 0.7463 (tt0) cc_final: 0.6535 (tt0) REVERT: A 121 ILE cc_start: 0.8314 (mp) cc_final: 0.7915 (mm) REVERT: A 123 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6522 (mm-30) REVERT: A 184 HIS cc_start: 0.6573 (m-70) cc_final: 0.5634 (m-70) REVERT: A 189 GLN cc_start: 0.7515 (mt0) cc_final: 0.7309 (mm-40) REVERT: A 233 TYR cc_start: 0.6314 (m-80) cc_final: 0.5952 (m-80) REVERT: A 261 ARG cc_start: 0.7527 (mtt90) cc_final: 0.7238 (mmt90) REVERT: A 275 ASP cc_start: 0.7142 (t0) cc_final: 0.6872 (t0) REVERT: B 25 ARG cc_start: 0.6933 (tmt170) cc_final: 0.6427 (tmt170) REVERT: B 79 ASP cc_start: 0.7237 (m-30) cc_final: 0.6922 (m-30) REVERT: B 89 ILE cc_start: 0.8482 (mt) cc_final: 0.8167 (mt) REVERT: B 91 LEU cc_start: 0.7419 (mt) cc_final: 0.6940 (mt) REVERT: B 94 TYR cc_start: 0.8496 (t80) cc_final: 0.7635 (t80) REVERT: B 95 ASN cc_start: 0.7789 (m110) cc_final: 0.7489 (m110) REVERT: B 115 MET cc_start: 0.6183 (tpp) cc_final: 0.5938 (tpp) REVERT: B 121 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7679 (tptp) REVERT: G 3 GLN cc_start: 0.6699 (mp-120) cc_final: 0.6190 (mp10) REVERT: G 34 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.5092 (mmp) REVERT: G 68 PHE cc_start: 0.7459 (m-80) cc_final: 0.7034 (m-80) REVERT: G 83 MET cc_start: 0.5542 (OUTLIER) cc_final: 0.4542 (mtp) REVERT: J 5 THR cc_start: 0.6989 (OUTLIER) cc_final: 0.6667 (t) REVERT: J 18 ARG cc_start: 0.7270 (ttm170) cc_final: 0.7062 (ttm170) REVERT: J 65 SER cc_start: 0.8505 (t) cc_final: 0.7995 (m) REVERT: J 148 TRP cc_start: 0.6205 (m100) cc_final: 0.5953 (m100) REVERT: C 71 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7796 (mt) REVERT: C 79 PHE cc_start: 0.7359 (m-10) cc_final: 0.7147 (m-80) REVERT: C 92 LYS cc_start: 0.8359 (pttp) cc_final: 0.8026 (pttp) REVERT: C 123 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6621 (mt-10) REVERT: C 153 TRP cc_start: 0.7142 (t60) cc_final: 0.6819 (t-100) REVERT: C 208 ARG cc_start: 0.7162 (mtt90) cc_final: 0.6566 (mtt90) REVERT: C 290 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7249 (p0) REVERT: C 296 ASN cc_start: 0.6934 (p0) cc_final: 0.6550 (t0) REVERT: E 25 ARG cc_start: 0.7115 (tmt170) cc_final: 0.6608 (tmt170) REVERT: E 42 GLN cc_start: 0.7550 (tp-100) cc_final: 0.7132 (tp-100) REVERT: E 62 LYS cc_start: 0.7401 (tttt) cc_final: 0.7048 (tttt) REVERT: E 79 ASP cc_start: 0.7499 (m-30) cc_final: 0.7235 (m-30) REVERT: E 85 GLU cc_start: 0.7276 (tp30) cc_final: 0.6905 (tp30) REVERT: E 91 LEU cc_start: 0.7675 (mt) cc_final: 0.7139 (mt) REVERT: E 95 ASN cc_start: 0.7998 (m-40) cc_final: 0.7576 (m-40) REVERT: E 102 LEU cc_start: 0.8194 (tp) cc_final: 0.7955 (tp) REVERT: E 110 LEU cc_start: 0.7441 (tp) cc_final: 0.7237 (tt) REVERT: E 121 LYS cc_start: 0.7841 (tptp) cc_final: 0.7625 (tptp) REVERT: E 133 MET cc_start: 0.6147 (ptp) cc_final: 0.5778 (ptm) REVERT: H 3 GLN cc_start: 0.6198 (mp10) cc_final: 0.5644 (mp10) REVERT: H 20 LEU cc_start: 0.7836 (mt) cc_final: 0.7581 (mt) REVERT: H 65 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8599 (mmmt) REVERT: H 117 MET cc_start: 0.7473 (mtm) cc_final: 0.6405 (mpp) REVERT: H 181 HIS cc_start: 0.6029 (m-70) cc_final: 0.5717 (m-70) REVERT: L 18 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7367 (ttm170) REVERT: L 35 TRP cc_start: 0.5750 (m100) cc_final: 0.5260 (m100) REVERT: L 74 THR cc_start: 0.7920 (m) cc_final: 0.7488 (p) REVERT: D 57 ARG cc_start: 0.7846 (ttt90) cc_final: 0.7455 (ttt90) REVERT: D 67 ILE cc_start: 0.7807 (mm) cc_final: 0.7162 (tp) REVERT: D 71 LEU cc_start: 0.7642 (mm) cc_final: 0.7229 (mm) REVERT: D 80 GLN cc_start: 0.6753 (tp40) cc_final: 0.6476 (tp40) REVERT: D 119 GLU cc_start: 0.7676 (tt0) cc_final: 0.7273 (tt0) REVERT: D 123 GLU cc_start: 0.6540 (mt-10) cc_final: 0.5755 (tt0) REVERT: D 141 ARG cc_start: 0.7550 (tpp-160) cc_final: 0.7159 (mmt180) REVERT: D 150 ARG cc_start: 0.7930 (mmm160) cc_final: 0.7562 (mmm160) REVERT: D 168 MET cc_start: 0.6550 (mmm) cc_final: 0.6109 (mmm) REVERT: D 184 HIS cc_start: 0.6834 (m-70) cc_final: 0.6346 (m-70) REVERT: D 186 SER cc_start: 0.7911 (p) cc_final: 0.7651 (m) REVERT: D 212 THR cc_start: 0.8380 (m) cc_final: 0.8124 (p) REVERT: D 314 LEU cc_start: 0.7662 (mt) cc_final: 0.7454 (mt) REVERT: F 25 ARG cc_start: 0.6522 (tmt170) cc_final: 0.6179 (tmt170) REVERT: F 79 ASP cc_start: 0.7220 (m-30) cc_final: 0.6817 (m-30) REVERT: F 85 GLU cc_start: 0.6779 (tp30) cc_final: 0.6446 (tp30) REVERT: F 89 ILE cc_start: 0.8251 (mt) cc_final: 0.7659 (mt) REVERT: F 97 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7200 (mt-10) outliers start: 122 outliers final: 96 residues processed: 671 average time/residue: 0.3424 time to fit residues: 345.5778 Evaluate side-chains 703 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 602 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 148 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 33 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN A 81 ASN ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 GLN ** C 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 21945 Z= 0.324 Angle : 0.691 12.541 29790 Z= 0.363 Chirality : 0.046 0.312 3309 Planarity : 0.005 0.056 3876 Dihedral : 5.577 59.471 3010 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.59 % Favored : 94.30 % Rotamer: Outliers : 5.40 % Allowed : 13.92 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % 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: -1.95 (0.15), residues: 2754 helix: -0.51 (0.25), residues: 372 sheet: -0.83 (0.17), residues: 816 loop : -1.78 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP H 36 HIS 0.015 0.002 HIS E 159 PHE 0.021 0.002 PHE C 125 TYR 0.023 0.002 TYR C 105 ARG 0.008 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 611 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: I 3 GLN cc_start: 0.6108 (mp-120) cc_final: 0.5837 (mm-40) REVERT: I 22 CYS cc_start: 0.5413 (t) cc_final: 0.4929 (t) REVERT: I 51 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5704 (tp) REVERT: I 68 PHE cc_start: 0.7738 (m-80) cc_final: 0.7130 (m-80) REVERT: I 83 MET cc_start: 0.5914 (mtp) cc_final: 0.4252 (mtp) REVERT: I 117 MET cc_start: 0.6739 (mtm) cc_final: 0.6412 (mtt) REVERT: I 171 TRP cc_start: 0.7019 (m100) cc_final: 0.6703 (m100) REVERT: I 181 HIS cc_start: 0.5530 (m-70) cc_final: 0.5105 (m-70) REVERT: K 11 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8424 (p) REVERT: K 62 PHE cc_start: 0.7308 (t80) cc_final: 0.6848 (t80) REVERT: K 63 SER cc_start: 0.7380 (m) cc_final: 0.6880 (t) REVERT: K 74 THR cc_start: 0.7808 (m) cc_final: 0.7124 (p) REVERT: K 147 GLN cc_start: 0.6560 (pp30) cc_final: 0.4624 (mp10) REVERT: K 149 LYS cc_start: 0.6882 (mmmt) cc_final: 0.6570 (mmmt) REVERT: K 176 SER cc_start: 0.7868 (t) cc_final: 0.7329 (p) REVERT: K 177 SER cc_start: 0.7384 (t) cc_final: 0.7032 (t) REVERT: K 189 HIS cc_start: 0.8018 (m-70) cc_final: 0.7698 (m-70) REVERT: K 210 ASN cc_start: 0.8489 (t0) cc_final: 0.8150 (p0) REVERT: A 75 HIS cc_start: 0.6483 (m-70) cc_final: 0.6037 (m-70) REVERT: A 119 GLU cc_start: 0.7459 (tt0) cc_final: 0.6462 (tt0) REVERT: A 121 ILE cc_start: 0.8335 (mp) cc_final: 0.7961 (mm) REVERT: A 123 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6579 (mm-30) REVERT: A 125 PHE cc_start: 0.6637 (m-80) cc_final: 0.6105 (m-80) REVERT: A 184 HIS cc_start: 0.6540 (m-70) cc_final: 0.6088 (m170) REVERT: A 208 ARG cc_start: 0.7275 (mtt90) cc_final: 0.6494 (mtt90) REVERT: A 233 TYR cc_start: 0.6555 (m-80) cc_final: 0.6075 (m-80) REVERT: A 261 ARG cc_start: 0.7487 (mtt90) cc_final: 0.7137 (mmt90) REVERT: A 268 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7702 (ttm) REVERT: A 275 ASP cc_start: 0.7117 (t0) cc_final: 0.6831 (t0) REVERT: B 25 ARG cc_start: 0.6882 (tmt170) cc_final: 0.6562 (tmt170) REVERT: B 79 ASP cc_start: 0.7236 (m-30) cc_final: 0.6901 (m-30) REVERT: B 91 LEU cc_start: 0.7484 (mt) cc_final: 0.7022 (mt) REVERT: B 94 TYR cc_start: 0.8440 (t80) cc_final: 0.7625 (t80) REVERT: B 95 ASN cc_start: 0.7868 (m110) cc_final: 0.7438 (m110) REVERT: B 115 MET cc_start: 0.6202 (tpp) cc_final: 0.5900 (tpp) REVERT: B 121 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7611 (tptp) REVERT: G 3 GLN cc_start: 0.6705 (mp-120) cc_final: 0.6168 (mp10) REVERT: G 34 MET cc_start: 0.5397 (mmp) cc_final: 0.5148 (mmp) REVERT: G 68 PHE cc_start: 0.7443 (m-80) cc_final: 0.6999 (m-80) REVERT: G 80 PHE cc_start: 0.7393 (m-80) cc_final: 0.6894 (m-80) REVERT: G 83 MET cc_start: 0.5480 (OUTLIER) cc_final: 0.4396 (mtp) REVERT: J 5 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6580 (t) REVERT: J 11 VAL cc_start: 0.8575 (p) cc_final: 0.8319 (m) REVERT: J 12 SER cc_start: 0.8330 (m) cc_final: 0.7811 (t) REVERT: J 65 SER cc_start: 0.8351 (t) cc_final: 0.7878 (m) REVERT: J 89 GLN cc_start: 0.6586 (pp30) cc_final: 0.6373 (pp30) REVERT: C 40 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.7962 (p) REVERT: C 71 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7848 (mt) REVERT: C 79 PHE cc_start: 0.7434 (m-10) cc_final: 0.7162 (m-80) REVERT: C 92 LYS cc_start: 0.8349 (pttp) cc_final: 0.8033 (pttp) REVERT: C 100 TYR cc_start: 0.7301 (p90) cc_final: 0.7039 (p90) REVERT: C 109 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7514 (mtp85) REVERT: C 123 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6794 (mt-10) REVERT: C 153 TRP cc_start: 0.7073 (t60) cc_final: 0.6748 (t-100) REVERT: C 189 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: C 208 ARG cc_start: 0.7176 (mtt90) cc_final: 0.6587 (mtt90) REVERT: C 296 ASN cc_start: 0.7200 (p0) cc_final: 0.6952 (p0) REVERT: E 25 ARG cc_start: 0.7125 (tmt170) cc_final: 0.6557 (tmt170) REVERT: E 42 GLN cc_start: 0.7529 (tp-100) cc_final: 0.6957 (tp-100) REVERT: E 62 LYS cc_start: 0.7245 (tttt) cc_final: 0.6992 (tttt) REVERT: E 79 ASP cc_start: 0.7520 (m-30) cc_final: 0.7261 (m-30) REVERT: E 85 GLU cc_start: 0.7267 (tp30) cc_final: 0.6921 (tp30) REVERT: E 91 LEU cc_start: 0.7572 (mt) cc_final: 0.7042 (mt) REVERT: E 95 ASN cc_start: 0.7953 (m-40) cc_final: 0.7535 (m-40) REVERT: E 110 LEU cc_start: 0.7412 (tp) cc_final: 0.7064 (tt) REVERT: E 121 LYS cc_start: 0.7739 (tptp) cc_final: 0.7518 (tptp) REVERT: E 133 MET cc_start: 0.6159 (ptp) cc_final: 0.5830 (ptm) REVERT: H 3 GLN cc_start: 0.6191 (mp10) cc_final: 0.5540 (mp10) REVERT: H 65 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8465 (tppp) REVERT: H 117 MET cc_start: 0.7096 (mtm) cc_final: 0.6736 (mtm) REVERT: H 181 HIS cc_start: 0.6092 (m-70) cc_final: 0.5781 (m-70) REVERT: L 18 ARG cc_start: 0.7581 (ttm170) cc_final: 0.7354 (ttm170) REVERT: L 27 GLN cc_start: 0.7100 (pp30) cc_final: 0.6760 (pp30) REVERT: L 74 THR cc_start: 0.7781 (m) cc_final: 0.7327 (p) REVERT: D 50 LYS cc_start: 0.7464 (mttt) cc_final: 0.7195 (mttt) REVERT: D 57 ARG cc_start: 0.7889 (ttt90) cc_final: 0.7172 (ttm-80) REVERT: D 67 ILE cc_start: 0.7789 (mm) cc_final: 0.7197 (tp) REVERT: D 71 LEU cc_start: 0.7643 (mm) cc_final: 0.7284 (mm) REVERT: D 82 GLU cc_start: 0.7599 (tp30) cc_final: 0.7220 (tp30) REVERT: D 119 GLU cc_start: 0.7608 (tt0) cc_final: 0.7165 (tt0) REVERT: D 123 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6075 (tt0) REVERT: D 141 ARG cc_start: 0.7563 (tpp-160) cc_final: 0.7161 (mmt180) REVERT: D 168 MET cc_start: 0.6644 (mmm) cc_final: 0.6252 (mmm) REVERT: D 184 HIS cc_start: 0.6801 (m-70) cc_final: 0.6330 (m-70) REVERT: D 186 SER cc_start: 0.7934 (p) cc_final: 0.7538 (m) REVERT: D 212 THR cc_start: 0.8497 (m) cc_final: 0.8211 (p) REVERT: F 14 TRP cc_start: 0.5936 (m100) cc_final: 0.5706 (m100) REVERT: F 85 GLU cc_start: 0.6785 (tp30) cc_final: 0.6479 (tp30) REVERT: F 89 ILE cc_start: 0.8231 (mt) cc_final: 0.7703 (mt) REVERT: F 97 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7258 (mt-10) outliers start: 130 outliers final: 96 residues processed: 667 average time/residue: 0.3414 time to fit residues: 345.0864 Evaluate side-chains 697 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 593 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 148 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 chunk 51 optimal weight: 0.0000 chunk 153 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 overall best weight: 0.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 33 ASN K 27 GLN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN C 290 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 GLN D 53 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21945 Z= 0.181 Angle : 0.606 10.595 29790 Z= 0.312 Chirality : 0.044 0.250 3309 Planarity : 0.004 0.076 3876 Dihedral : 5.084 58.867 3010 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.63 % Favored : 96.26 % Rotamer: Outliers : 3.78 % Allowed : 16.33 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % 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: -1.58 (0.15), residues: 2754 helix: -0.06 (0.26), residues: 369 sheet: -0.63 (0.17), residues: 810 loop : -1.54 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 36 HIS 0.006 0.001 HIS K 87 PHE 0.029 0.002 PHE G 29 TYR 0.018 0.001 TYR J 36 ARG 0.005 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 606 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: I 3 GLN cc_start: 0.6190 (mp-120) cc_final: 0.5868 (mm-40) REVERT: I 51 ILE cc_start: 0.6027 (OUTLIER) cc_final: 0.5713 (tp) REVERT: I 68 PHE cc_start: 0.7616 (m-80) cc_final: 0.7070 (m-80) REVERT: I 70 ILE cc_start: 0.8198 (pt) cc_final: 0.7890 (mp) REVERT: I 83 MET cc_start: 0.5783 (mtp) cc_final: 0.4019 (mtp) REVERT: I 117 MET cc_start: 0.6749 (mtm) cc_final: 0.6425 (mtt) REVERT: I 181 HIS cc_start: 0.5612 (m-70) cc_final: 0.5156 (m-70) REVERT: K 62 PHE cc_start: 0.7181 (t80) cc_final: 0.6763 (t80) REVERT: K 63 SER cc_start: 0.7338 (m) cc_final: 0.6685 (t) REVERT: K 74 THR cc_start: 0.7880 (m) cc_final: 0.7129 (p) REVERT: K 85 THR cc_start: 0.5225 (m) cc_final: 0.4485 (p) REVERT: K 147 GLN cc_start: 0.6478 (pp30) cc_final: 0.4814 (mp10) REVERT: K 176 SER cc_start: 0.7816 (OUTLIER) cc_final: 0.7341 (p) REVERT: K 177 SER cc_start: 0.7309 (t) cc_final: 0.6952 (t) REVERT: K 189 HIS cc_start: 0.7939 (m-70) cc_final: 0.7725 (m-70) REVERT: K 210 ASN cc_start: 0.8454 (t0) cc_final: 0.8103 (p0) REVERT: A 57 ARG cc_start: 0.7530 (ttt90) cc_final: 0.6878 (ttm-80) REVERT: A 75 HIS cc_start: 0.6781 (m-70) cc_final: 0.6344 (m-70) REVERT: A 119 GLU cc_start: 0.7398 (tt0) cc_final: 0.6393 (tt0) REVERT: A 121 ILE cc_start: 0.8360 (mp) cc_final: 0.8027 (mm) REVERT: A 123 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6499 (mm-30) REVERT: A 125 PHE cc_start: 0.6687 (m-80) cc_final: 0.6193 (m-80) REVERT: A 208 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6465 (mtt90) REVERT: A 233 TYR cc_start: 0.6388 (m-80) cc_final: 0.5926 (m-80) REVERT: A 261 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7105 (mmt90) REVERT: A 275 ASP cc_start: 0.7065 (t0) cc_final: 0.6742 (t0) REVERT: B 79 ASP cc_start: 0.7166 (m-30) cc_final: 0.6837 (m-30) REVERT: B 91 LEU cc_start: 0.7452 (mt) cc_final: 0.7011 (mt) REVERT: B 94 TYR cc_start: 0.8340 (t80) cc_final: 0.7659 (t80) REVERT: B 95 ASN cc_start: 0.7874 (m110) cc_final: 0.7565 (m110) REVERT: B 115 MET cc_start: 0.6182 (tpp) cc_final: 0.5841 (tpp) REVERT: B 121 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7509 (tptp) REVERT: G 3 GLN cc_start: 0.6645 (mp-120) cc_final: 0.6082 (mp10) REVERT: G 68 PHE cc_start: 0.7343 (m-80) cc_final: 0.6862 (m-80) REVERT: G 80 PHE cc_start: 0.7368 (m-80) cc_final: 0.6830 (m-80) REVERT: G 83 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.4269 (mtp) REVERT: J 5 THR cc_start: 0.6839 (OUTLIER) cc_final: 0.6547 (t) REVERT: J 6 GLN cc_start: 0.5400 (mp10) cc_final: 0.4738 (mp10) REVERT: J 11 VAL cc_start: 0.8668 (p) cc_final: 0.8429 (m) REVERT: J 12 SER cc_start: 0.8266 (m) cc_final: 0.7732 (t) REVERT: J 20 THR cc_start: 0.8357 (m) cc_final: 0.8083 (t) REVERT: J 46 LEU cc_start: 0.4620 (tp) cc_final: 0.4121 (tp) REVERT: J 65 SER cc_start: 0.8359 (t) cc_final: 0.7916 (m) REVERT: J 179 LEU cc_start: 0.7703 (tp) cc_final: 0.7396 (tp) REVERT: C 71 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7809 (mt) REVERT: C 79 PHE cc_start: 0.7116 (m-10) cc_final: 0.6882 (m-80) REVERT: C 92 LYS cc_start: 0.8334 (pttp) cc_final: 0.8012 (pttp) REVERT: C 109 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7081 (ttt-90) REVERT: C 121 ILE cc_start: 0.8632 (mm) cc_final: 0.8303 (mp) REVERT: C 123 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6837 (mt-10) REVERT: C 153 TRP cc_start: 0.6969 (t60) cc_final: 0.6620 (t-100) REVERT: C 189 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7072 (mm-40) REVERT: C 208 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6572 (mtt90) REVERT: C 290 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.6971 (p0) REVERT: C 315 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6961 (mmtt) REVERT: E 25 ARG cc_start: 0.7003 (tmt170) cc_final: 0.6680 (tmt170) REVERT: E 42 GLN cc_start: 0.7657 (tp-100) cc_final: 0.7225 (tp-100) REVERT: E 79 ASP cc_start: 0.7292 (m-30) cc_final: 0.7048 (m-30) REVERT: E 85 GLU cc_start: 0.7030 (tp30) cc_final: 0.6705 (tp30) REVERT: E 91 LEU cc_start: 0.7605 (mt) cc_final: 0.7139 (mt) REVERT: E 95 ASN cc_start: 0.7898 (m-40) cc_final: 0.7402 (m-40) REVERT: E 102 LEU cc_start: 0.8041 (tp) cc_final: 0.7787 (tp) REVERT: E 121 LYS cc_start: 0.7747 (tptp) cc_final: 0.7500 (tptp) REVERT: E 133 MET cc_start: 0.6010 (ptp) cc_final: 0.5655 (ptm) REVERT: H 3 GLN cc_start: 0.6204 (mp10) cc_final: 0.5542 (mp10) REVERT: H 65 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8356 (tppp) REVERT: H 72 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7652 (ttm170) REVERT: H 112 TYR cc_start: 0.5514 (m-10) cc_final: 0.5233 (m-10) REVERT: H 117 MET cc_start: 0.6956 (mtm) cc_final: 0.6139 (mpp) REVERT: H 181 HIS cc_start: 0.6050 (m-70) cc_final: 0.5753 (m-70) REVERT: L 18 ARG cc_start: 0.7534 (ttm170) cc_final: 0.7325 (ttm170) REVERT: L 27 GLN cc_start: 0.6720 (pp30) cc_final: 0.6208 (pp30) REVERT: L 74 THR cc_start: 0.7656 (m) cc_final: 0.7258 (p) REVERT: D 35 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.6045 (mp0) REVERT: D 50 LYS cc_start: 0.7415 (mttt) cc_final: 0.7160 (mttt) REVERT: D 57 ARG cc_start: 0.7840 (ttt90) cc_final: 0.7397 (ttm-80) REVERT: D 67 ILE cc_start: 0.7724 (mm) cc_final: 0.7099 (tp) REVERT: D 71 LEU cc_start: 0.7663 (mm) cc_final: 0.7232 (mm) REVERT: D 119 GLU cc_start: 0.7517 (tt0) cc_final: 0.7025 (tt0) REVERT: D 168 MET cc_start: 0.6540 (mmm) cc_final: 0.6187 (mmm) REVERT: D 186 SER cc_start: 0.7989 (p) cc_final: 0.7594 (m) REVERT: D 212 THR cc_start: 0.8382 (m) cc_final: 0.8082 (p) REVERT: F 14 TRP cc_start: 0.5634 (m100) cc_final: 0.5351 (m100) REVERT: F 25 ARG cc_start: 0.6964 (tmt170) cc_final: 0.6656 (tmt170) REVERT: F 41 THR cc_start: 0.7446 (m) cc_final: 0.7122 (m) REVERT: F 81 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: F 85 GLU cc_start: 0.6715 (tp30) cc_final: 0.6419 (tp30) REVERT: F 89 ILE cc_start: 0.8204 (mt) cc_final: 0.7657 (mt) REVERT: F 121 LYS cc_start: 0.7901 (tptp) cc_final: 0.7666 (tptp) outliers start: 91 outliers final: 61 residues processed: 646 average time/residue: 0.3663 time to fit residues: 358.5714 Evaluate side-chains 647 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 576 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 90 GLN Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 190 optimal weight: 0.2980 chunk 147 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 33 ASN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 GLN ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21945 Z= 0.208 Angle : 0.619 12.033 29790 Z= 0.321 Chirality : 0.045 0.372 3309 Planarity : 0.004 0.061 3876 Dihedral : 5.066 59.478 3010 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 3.45 % Allowed : 17.46 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 2754 helix: 0.08 (0.26), residues: 369 sheet: -0.55 (0.18), residues: 822 loop : -1.50 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 36 HIS 0.006 0.001 HIS E 159 PHE 0.043 0.002 PHE K 94 TYR 0.016 0.001 TYR J 173 ARG 0.007 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 599 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: I 3 GLN cc_start: 0.6209 (mp-120) cc_final: 0.5877 (mm-40) REVERT: I 22 CYS cc_start: 0.6555 (t) cc_final: 0.6246 (t) REVERT: I 51 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5642 (tp) REVERT: I 68 PHE cc_start: 0.7594 (m-80) cc_final: 0.7133 (m-80) REVERT: I 83 MET cc_start: 0.5785 (mtp) cc_final: 0.4284 (mtp) REVERT: I 108 TYR cc_start: 0.6012 (m-80) cc_final: 0.5582 (m-80) REVERT: I 117 MET cc_start: 0.6756 (mtm) cc_final: 0.6047 (mtt) REVERT: I 181 HIS cc_start: 0.5612 (m-70) cc_final: 0.5167 (m-70) REVERT: K 27 GLN cc_start: 0.6253 (pp30) cc_final: 0.6003 (pp30) REVERT: K 62 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6684 (t80) REVERT: K 63 SER cc_start: 0.7332 (m) cc_final: 0.6678 (t) REVERT: K 74 THR cc_start: 0.7923 (m) cc_final: 0.7188 (p) REVERT: K 176 SER cc_start: 0.7834 (t) cc_final: 0.7348 (p) REVERT: K 177 SER cc_start: 0.7410 (t) cc_final: 0.7054 (t) REVERT: K 210 ASN cc_start: 0.8455 (t0) cc_final: 0.8064 (p0) REVERT: A 75 HIS cc_start: 0.6797 (m-70) cc_final: 0.6341 (m-70) REVERT: A 119 GLU cc_start: 0.7438 (tt0) cc_final: 0.6464 (tt0) REVERT: A 121 ILE cc_start: 0.8349 (mp) cc_final: 0.8011 (mm) REVERT: A 123 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6505 (mm-30) REVERT: A 125 PHE cc_start: 0.6634 (m-80) cc_final: 0.6380 (m-10) REVERT: A 208 ARG cc_start: 0.7234 (mtt90) cc_final: 0.6460 (mtt90) REVERT: A 223 VAL cc_start: 0.7514 (t) cc_final: 0.7237 (p) REVERT: A 233 TYR cc_start: 0.6414 (m-80) cc_final: 0.5975 (m-80) REVERT: A 242 VAL cc_start: 0.7202 (OUTLIER) cc_final: 0.6993 (m) REVERT: A 261 ARG cc_start: 0.7403 (mtt90) cc_final: 0.7129 (mmt90) REVERT: A 275 ASP cc_start: 0.7015 (t0) cc_final: 0.6726 (t0) REVERT: B 79 ASP cc_start: 0.7160 (m-30) cc_final: 0.6837 (m-30) REVERT: B 91 LEU cc_start: 0.7499 (mt) cc_final: 0.7050 (mt) REVERT: B 94 TYR cc_start: 0.8372 (t80) cc_final: 0.7583 (t80) REVERT: B 95 ASN cc_start: 0.7905 (m110) cc_final: 0.7532 (m110) REVERT: B 115 MET cc_start: 0.6224 (tpp) cc_final: 0.5856 (tpp) REVERT: B 121 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7496 (tptp) REVERT: G 3 GLN cc_start: 0.6637 (mp-120) cc_final: 0.6092 (mp10) REVERT: G 68 PHE cc_start: 0.7345 (m-80) cc_final: 0.6859 (m-80) REVERT: G 83 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.4272 (mtp) REVERT: J 5 THR cc_start: 0.6896 (OUTLIER) cc_final: 0.6490 (m) REVERT: J 11 VAL cc_start: 0.8679 (p) cc_final: 0.8444 (m) REVERT: J 12 SER cc_start: 0.8288 (m) cc_final: 0.7757 (t) REVERT: J 46 LEU cc_start: 0.4633 (tp) cc_final: 0.4147 (tp) REVERT: J 65 SER cc_start: 0.8322 (t) cc_final: 0.7872 (m) REVERT: C 71 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7829 (mt) REVERT: C 79 PHE cc_start: 0.7057 (m-10) cc_final: 0.6824 (m-80) REVERT: C 92 LYS cc_start: 0.8362 (pttp) cc_final: 0.8047 (pttp) REVERT: C 109 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.6967 (ttt-90) REVERT: C 121 ILE cc_start: 0.8632 (mm) cc_final: 0.8301 (mp) REVERT: C 153 TRP cc_start: 0.6948 (t60) cc_final: 0.6694 (t60) REVERT: C 161 TYR cc_start: 0.7213 (t80) cc_final: 0.6946 (t80) REVERT: C 164 LEU cc_start: 0.7286 (mt) cc_final: 0.7063 (mp) REVERT: C 189 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.7075 (mm-40) REVERT: C 194 LEU cc_start: 0.7453 (tp) cc_final: 0.7212 (tp) REVERT: C 208 ARG cc_start: 0.7151 (mtt90) cc_final: 0.6553 (mtt90) REVERT: C 315 LYS cc_start: 0.7231 (mmtt) cc_final: 0.6960 (mmtt) REVERT: E 25 ARG cc_start: 0.7006 (tmt170) cc_final: 0.6627 (tmt170) REVERT: E 42 GLN cc_start: 0.7463 (tp40) cc_final: 0.7024 (tp-100) REVERT: E 79 ASP cc_start: 0.7394 (m-30) cc_final: 0.7141 (m-30) REVERT: E 85 GLU cc_start: 0.7126 (tp30) cc_final: 0.6772 (tp30) REVERT: E 91 LEU cc_start: 0.7637 (mt) cc_final: 0.7175 (mt) REVERT: E 95 ASN cc_start: 0.7893 (m-40) cc_final: 0.7271 (m-40) REVERT: E 102 LEU cc_start: 0.8115 (tp) cc_final: 0.7850 (tp) REVERT: E 121 LYS cc_start: 0.7741 (tptp) cc_final: 0.7470 (tptp) REVERT: E 133 MET cc_start: 0.6139 (ptp) cc_final: 0.5830 (ptm) REVERT: H 3 GLN cc_start: 0.6218 (mp10) cc_final: 0.5589 (mp10) REVERT: H 65 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8327 (tppp) REVERT: H 117 MET cc_start: 0.7002 (mtm) cc_final: 0.6000 (mpp) REVERT: H 181 HIS cc_start: 0.6059 (m-70) cc_final: 0.5795 (m-70) REVERT: L 6 GLN cc_start: 0.6920 (mm-40) cc_final: 0.6612 (mm-40) REVERT: L 18 ARG cc_start: 0.7545 (ttm170) cc_final: 0.7286 (ttm170) REVERT: L 27 GLN cc_start: 0.6718 (pp30) cc_final: 0.6235 (pp30) REVERT: L 74 THR cc_start: 0.7672 (m) cc_final: 0.7267 (p) REVERT: L 176 SER cc_start: 0.6909 (t) cc_final: 0.6520 (p) REVERT: D 57 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7567 (ttm-80) REVERT: D 67 ILE cc_start: 0.7710 (mm) cc_final: 0.7068 (tp) REVERT: D 71 LEU cc_start: 0.7646 (mm) cc_final: 0.7162 (mm) REVERT: D 81 ASN cc_start: 0.7215 (t0) cc_final: 0.6998 (t0) REVERT: D 82 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6386 (mt-10) REVERT: D 119 GLU cc_start: 0.7563 (tt0) cc_final: 0.7062 (tt0) REVERT: D 141 ARG cc_start: 0.7580 (tpp-160) cc_final: 0.7092 (mmt180) REVERT: D 168 MET cc_start: 0.6385 (mmm) cc_final: 0.6125 (mmm) REVERT: D 186 SER cc_start: 0.8024 (p) cc_final: 0.7615 (m) REVERT: D 212 THR cc_start: 0.8454 (m) cc_final: 0.8081 (p) REVERT: F 14 TRP cc_start: 0.5746 (m100) cc_final: 0.5449 (m100) REVERT: F 25 ARG cc_start: 0.6950 (tmt170) cc_final: 0.6630 (tmt170) REVERT: F 81 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7039 (pt0) REVERT: F 85 GLU cc_start: 0.6774 (tp30) cc_final: 0.6414 (tp30) REVERT: F 88 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8044 (ttpt) REVERT: F 89 ILE cc_start: 0.8373 (mt) cc_final: 0.7766 (mt) REVERT: F 121 LYS cc_start: 0.7870 (tptp) cc_final: 0.7604 (tptp) outliers start: 83 outliers final: 65 residues processed: 637 average time/residue: 0.3478 time to fit residues: 331.2417 Evaluate side-chains 650 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 577 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 164 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 165 optimal weight: 0.2980 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 33 ASN K 27 GLN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 290 ASN ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21945 Z= 0.290 Angle : 0.663 10.752 29790 Z= 0.346 Chirality : 0.046 0.280 3309 Planarity : 0.005 0.058 3876 Dihedral : 5.360 59.872 3010 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.19 % Rotamer: Outliers : 3.99 % Allowed : 17.29 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 2754 helix: 0.04 (0.26), residues: 363 sheet: -0.46 (0.18), residues: 813 loop : -1.54 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP H 36 HIS 0.008 0.001 HIS J 87 PHE 0.027 0.002 PHE H 27 TYR 0.018 0.002 TYR J 49 ARG 0.006 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 580 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.6120 (mp-120) cc_final: 0.5733 (mm-40) REVERT: I 68 PHE cc_start: 0.7585 (m-80) cc_final: 0.6962 (m-80) REVERT: I 83 MET cc_start: 0.5845 (mtp) cc_final: 0.4363 (mtp) REVERT: I 108 TYR cc_start: 0.5971 (m-80) cc_final: 0.5238 (m-80) REVERT: I 117 MET cc_start: 0.6663 (mtm) cc_final: 0.6338 (mtt) REVERT: I 181 HIS cc_start: 0.5700 (m-70) cc_final: 0.5262 (m-70) REVERT: I 217 HIS cc_start: 0.6440 (t-170) cc_final: 0.4943 (t-90) REVERT: K 11 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8403 (m) REVERT: K 35 TRP cc_start: 0.5743 (m100) cc_final: 0.5461 (m100) REVERT: K 62 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6715 (t80) REVERT: K 63 SER cc_start: 0.7401 (m) cc_final: 0.6807 (t) REVERT: K 74 THR cc_start: 0.7955 (m) cc_final: 0.7224 (p) REVERT: K 147 GLN cc_start: 0.6636 (pp30) cc_final: 0.5037 (mp10) REVERT: K 176 SER cc_start: 0.7911 (t) cc_final: 0.7440 (p) REVERT: K 177 SER cc_start: 0.7446 (t) cc_final: 0.7092 (t) REVERT: K 210 ASN cc_start: 0.8482 (t0) cc_final: 0.8042 (p0) REVERT: A 75 HIS cc_start: 0.6831 (m-70) cc_final: 0.6363 (m-70) REVERT: A 119 GLU cc_start: 0.7477 (tt0) cc_final: 0.6483 (tt0) REVERT: A 121 ILE cc_start: 0.8306 (mp) cc_final: 0.8019 (mm) REVERT: A 123 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6891 (mm-30) REVERT: A 125 PHE cc_start: 0.6746 (m-80) cc_final: 0.6366 (m-10) REVERT: A 208 ARG cc_start: 0.7224 (mtt90) cc_final: 0.6462 (mtt90) REVERT: A 223 VAL cc_start: 0.7464 (t) cc_final: 0.7185 (p) REVERT: A 233 TYR cc_start: 0.6534 (m-80) cc_final: 0.6096 (m-80) REVERT: A 242 VAL cc_start: 0.7140 (OUTLIER) cc_final: 0.6933 (m) REVERT: A 261 ARG cc_start: 0.7448 (mtt90) cc_final: 0.7175 (mmt90) REVERT: A 275 ASP cc_start: 0.7065 (t0) cc_final: 0.6778 (t0) REVERT: B 79 ASP cc_start: 0.7202 (m-30) cc_final: 0.6894 (m-30) REVERT: B 91 LEU cc_start: 0.7688 (mt) cc_final: 0.7216 (mt) REVERT: B 94 TYR cc_start: 0.8378 (t80) cc_final: 0.7602 (t80) REVERT: B 95 ASN cc_start: 0.7937 (m110) cc_final: 0.7550 (m110) REVERT: B 115 MET cc_start: 0.6268 (tpp) cc_final: 0.5909 (tpp) REVERT: B 121 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7527 (tptp) REVERT: G 3 GLN cc_start: 0.6475 (mp-120) cc_final: 0.5748 (mp-120) REVERT: G 68 PHE cc_start: 0.7433 (m-80) cc_final: 0.6917 (m-80) REVERT: G 83 MET cc_start: 0.5529 (OUTLIER) cc_final: 0.4237 (mtp) REVERT: J 5 THR cc_start: 0.7136 (OUTLIER) cc_final: 0.5677 (t) REVERT: J 11 VAL cc_start: 0.8717 (p) cc_final: 0.8477 (m) REVERT: J 12 SER cc_start: 0.8345 (m) cc_final: 0.7808 (t) REVERT: J 46 LEU cc_start: 0.5078 (tp) cc_final: 0.4546 (tp) REVERT: J 65 SER cc_start: 0.8319 (t) cc_final: 0.7884 (m) REVERT: J 189 HIS cc_start: 0.8070 (m-70) cc_final: 0.7776 (m-70) REVERT: C 71 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7865 (mt) REVERT: C 79 PHE cc_start: 0.7193 (m-10) cc_final: 0.6903 (m-80) REVERT: C 109 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7232 (ttt-90) REVERT: C 121 ILE cc_start: 0.8604 (mm) cc_final: 0.8288 (mp) REVERT: C 153 TRP cc_start: 0.7008 (t60) cc_final: 0.6773 (t60) REVERT: C 164 LEU cc_start: 0.7171 (mt) cc_final: 0.6909 (mp) REVERT: C 189 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7132 (mm-40) REVERT: C 208 ARG cc_start: 0.7176 (mtt90) cc_final: 0.6561 (mtt90) REVERT: C 259 LYS cc_start: 0.7847 (mttt) cc_final: 0.7594 (mttm) REVERT: C 290 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6918 (p0) REVERT: C 315 LYS cc_start: 0.7389 (mmtt) cc_final: 0.7104 (mmtt) REVERT: E 14 TRP cc_start: 0.6394 (m100) cc_final: 0.6082 (m100) REVERT: E 25 ARG cc_start: 0.6979 (tmt170) cc_final: 0.6731 (tmt170) REVERT: E 42 GLN cc_start: 0.7504 (tp40) cc_final: 0.7143 (tp-100) REVERT: E 62 LYS cc_start: 0.7232 (tttt) cc_final: 0.7016 (tttt) REVERT: E 65 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6502 (mm-40) REVERT: E 79 ASP cc_start: 0.7550 (m-30) cc_final: 0.7266 (m-30) REVERT: E 85 GLU cc_start: 0.7142 (tp30) cc_final: 0.6834 (tp30) REVERT: E 91 LEU cc_start: 0.7548 (mt) cc_final: 0.7013 (mt) REVERT: E 95 ASN cc_start: 0.7967 (m-40) cc_final: 0.7531 (m-40) REVERT: E 102 LEU cc_start: 0.8136 (tp) cc_final: 0.7898 (tp) REVERT: E 114 GLU cc_start: 0.6388 (mm-30) cc_final: 0.5302 (mm-30) REVERT: E 117 LYS cc_start: 0.7938 (mttp) cc_final: 0.7735 (mttp) REVERT: E 121 LYS cc_start: 0.7835 (tptp) cc_final: 0.7573 (tptp) REVERT: H 3 GLN cc_start: 0.6238 (mp10) cc_final: 0.5546 (mp10) REVERT: H 65 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8401 (tppp) REVERT: H 117 MET cc_start: 0.7119 (mtm) cc_final: 0.6371 (mpp) REVERT: H 181 HIS cc_start: 0.6088 (m-70) cc_final: 0.5832 (m-70) REVERT: L 6 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6895 (mm-40) REVERT: L 18 ARG cc_start: 0.7589 (ttm170) cc_final: 0.7331 (ttm170) REVERT: L 27 GLN cc_start: 0.6813 (pp30) cc_final: 0.6479 (pp30) REVERT: L 74 THR cc_start: 0.7773 (m) cc_final: 0.7310 (p) REVERT: L 89 GLN cc_start: 0.5786 (tt0) cc_final: 0.5094 (tt0) REVERT: L 176 SER cc_start: 0.7013 (t) cc_final: 0.6589 (p) REVERT: D 57 ARG cc_start: 0.8004 (ttt90) cc_final: 0.7545 (ttm-80) REVERT: D 67 ILE cc_start: 0.7727 (mm) cc_final: 0.7063 (tp) REVERT: D 71 LEU cc_start: 0.7614 (mm) cc_final: 0.7146 (mm) REVERT: D 81 ASN cc_start: 0.7117 (t0) cc_final: 0.6865 (t0) REVERT: D 82 GLU cc_start: 0.6602 (mt-10) cc_final: 0.5965 (mp0) REVERT: D 119 GLU cc_start: 0.7603 (tt0) cc_final: 0.7096 (tt0) REVERT: D 127 TRP cc_start: 0.8152 (m-90) cc_final: 0.6684 (m-90) REVERT: D 186 SER cc_start: 0.7888 (p) cc_final: 0.7515 (m) REVERT: D 212 THR cc_start: 0.8416 (m) cc_final: 0.8134 (p) REVERT: F 14 TRP cc_start: 0.5963 (m100) cc_final: 0.5701 (m100) REVERT: F 25 ARG cc_start: 0.6809 (tmt170) cc_final: 0.6472 (tmt170) REVERT: F 81 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7173 (pt0) REVERT: F 85 GLU cc_start: 0.6865 (tp30) cc_final: 0.6528 (tp30) REVERT: F 88 LYS cc_start: 0.8250 (ttmt) cc_final: 0.8010 (ttpt) REVERT: F 89 ILE cc_start: 0.8520 (mt) cc_final: 0.8038 (mt) REVERT: F 121 LYS cc_start: 0.7889 (tptp) cc_final: 0.7570 (tptp) outliers start: 96 outliers final: 72 residues processed: 622 average time/residue: 0.3468 time to fit residues: 322.4707 Evaluate side-chains 656 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 574 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 227 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 190 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 33 ASN K 27 GLN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN A 53 ASN A 183 HIS ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS C 80 GLN C 184 HIS ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN F 42 GLN F 106 HIS F 146 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 21945 Z= 0.437 Angle : 0.790 11.659 29790 Z= 0.418 Chirality : 0.049 0.292 3309 Planarity : 0.006 0.080 3876 Dihedral : 6.014 58.004 3010 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.52 % Favored : 92.37 % Rotamer: Outliers : 4.45 % Allowed : 17.54 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2754 helix: -0.49 (0.26), residues: 369 sheet: -0.70 (0.18), residues: 825 loop : -1.78 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP H 36 HIS 0.011 0.002 HIS J 87 PHE 0.030 0.002 PHE H 27 TYR 0.027 0.003 TYR J 86 ARG 0.010 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 601 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.5837 (mp-120) cc_final: 0.5488 (mm-40) REVERT: I 68 PHE cc_start: 0.7629 (m-80) cc_final: 0.6965 (m-80) REVERT: I 83 MET cc_start: 0.5930 (mtp) cc_final: 0.4424 (mtp) REVERT: I 108 TYR cc_start: 0.6099 (m-80) cc_final: 0.5296 (m-80) REVERT: I 117 MET cc_start: 0.6836 (mtm) cc_final: 0.6417 (mtt) REVERT: K 62 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6591 (m-80) REVERT: K 85 THR cc_start: 0.5238 (m) cc_final: 0.4459 (p) REVERT: K 147 GLN cc_start: 0.6675 (pp30) cc_final: 0.4836 (mp10) REVERT: K 176 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7595 (p) REVERT: K 177 SER cc_start: 0.7516 (t) cc_final: 0.7199 (t) REVERT: K 210 ASN cc_start: 0.8487 (t0) cc_final: 0.8019 (p0) REVERT: A 75 HIS cc_start: 0.6445 (m-70) cc_final: 0.6018 (m-70) REVERT: A 92 LYS cc_start: 0.8857 (pttp) cc_final: 0.8386 (pttp) REVERT: A 119 GLU cc_start: 0.7491 (tt0) cc_final: 0.6361 (tt0) REVERT: A 121 ILE cc_start: 0.8359 (mp) cc_final: 0.7896 (mp) REVERT: A 125 PHE cc_start: 0.6820 (m-80) cc_final: 0.6505 (m-10) REVERT: A 208 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6459 (mtt90) REVERT: A 223 VAL cc_start: 0.7265 (t) cc_final: 0.7036 (p) REVERT: A 260 MET cc_start: 0.7030 (mmm) cc_final: 0.6398 (mpp) REVERT: A 261 ARG cc_start: 0.7357 (mtt90) cc_final: 0.7055 (mmt90) REVERT: A 275 ASP cc_start: 0.7098 (t0) cc_final: 0.6837 (t0) REVERT: B 79 ASP cc_start: 0.7361 (m-30) cc_final: 0.7000 (m-30) REVERT: B 91 LEU cc_start: 0.7635 (mt) cc_final: 0.7087 (mt) REVERT: B 94 TYR cc_start: 0.8429 (t80) cc_final: 0.7736 (t80) REVERT: B 95 ASN cc_start: 0.7963 (m110) cc_final: 0.7607 (m110) REVERT: B 115 MET cc_start: 0.6430 (tpp) cc_final: 0.6031 (tpp) REVERT: B 121 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7543 (tptp) REVERT: G 3 GLN cc_start: 0.6249 (mp-120) cc_final: 0.5589 (mp10) REVERT: G 68 PHE cc_start: 0.7610 (m-80) cc_final: 0.6990 (m-80) REVERT: G 70 ILE cc_start: 0.8403 (tt) cc_final: 0.8201 (pt) REVERT: G 83 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.4363 (mtp) REVERT: G 104 SER cc_start: 0.8276 (t) cc_final: 0.7919 (t) REVERT: J 11 VAL cc_start: 0.8588 (p) cc_final: 0.8365 (m) REVERT: J 12 SER cc_start: 0.8385 (m) cc_final: 0.7864 (t) REVERT: J 46 LEU cc_start: 0.5476 (tp) cc_final: 0.4991 (tp) REVERT: J 65 SER cc_start: 0.8248 (t) cc_final: 0.7784 (m) REVERT: J 189 HIS cc_start: 0.8143 (m-70) cc_final: 0.7846 (m-70) REVERT: C 71 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7918 (mt) REVERT: C 109 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7157 (mtp-110) REVERT: C 120 PHE cc_start: 0.7254 (t80) cc_final: 0.6589 (t80) REVERT: C 121 ILE cc_start: 0.8588 (mm) cc_final: 0.8244 (mp) REVERT: C 153 TRP cc_start: 0.7107 (t60) cc_final: 0.6891 (t60) REVERT: C 164 LEU cc_start: 0.7270 (mt) cc_final: 0.7021 (mp) REVERT: C 189 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7216 (mm-40) REVERT: C 260 MET cc_start: 0.7154 (mmm) cc_final: 0.6934 (mmt) REVERT: C 290 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6937 (p0) REVERT: E 42 GLN cc_start: 0.7582 (tp40) cc_final: 0.7204 (tp-100) REVERT: E 65 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6583 (mm-40) REVERT: E 79 ASP cc_start: 0.7796 (m-30) cc_final: 0.7475 (m-30) REVERT: E 85 GLU cc_start: 0.7174 (tp30) cc_final: 0.6880 (tp30) REVERT: E 91 LEU cc_start: 0.7611 (mt) cc_final: 0.7095 (mt) REVERT: E 95 ASN cc_start: 0.8067 (m-40) cc_final: 0.7621 (m-40) REVERT: E 114 GLU cc_start: 0.6665 (mm-30) cc_final: 0.5808 (mm-30) REVERT: E 117 LYS cc_start: 0.8006 (mttp) cc_final: 0.7770 (mttp) REVERT: E 121 LYS cc_start: 0.7726 (tptp) cc_final: 0.7481 (tptp) REVERT: E 150 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7549 (mt-10) REVERT: H 3 GLN cc_start: 0.6238 (mp10) cc_final: 0.5548 (mp10) REVERT: H 65 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8541 (tppp) REVERT: H 117 MET cc_start: 0.6899 (mtm) cc_final: 0.6510 (mtm) REVERT: L 18 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7288 (ttm170) REVERT: L 20 THR cc_start: 0.8657 (m) cc_final: 0.8320 (t) REVERT: L 35 TRP cc_start: 0.5539 (m100) cc_final: 0.5171 (m100) REVERT: L 74 THR cc_start: 0.7989 (m) cc_final: 0.7517 (p) REVERT: L 176 SER cc_start: 0.7122 (t) cc_final: 0.6656 (p) REVERT: D 50 LYS cc_start: 0.7492 (mttt) cc_final: 0.6982 (mttt) REVERT: D 67 ILE cc_start: 0.7780 (mm) cc_final: 0.7151 (tp) REVERT: D 71 LEU cc_start: 0.7641 (mm) cc_final: 0.7248 (mm) REVERT: D 119 GLU cc_start: 0.7689 (tt0) cc_final: 0.7414 (tp30) REVERT: D 186 SER cc_start: 0.7900 (p) cc_final: 0.7514 (m) REVERT: D 212 THR cc_start: 0.8507 (m) cc_final: 0.8225 (p) REVERT: D 287 SER cc_start: 0.8028 (m) cc_final: 0.7523 (p) REVERT: F 25 ARG cc_start: 0.6951 (tmt170) cc_final: 0.6539 (tmt170) REVERT: F 41 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7456 (p) REVERT: F 42 GLN cc_start: 0.7557 (tp40) cc_final: 0.7343 (tp-100) REVERT: F 51 LYS cc_start: 0.8049 (mttt) cc_final: 0.7818 (mttt) REVERT: F 85 GLU cc_start: 0.6876 (tp30) cc_final: 0.6612 (tp30) REVERT: F 89 ILE cc_start: 0.8616 (mt) cc_final: 0.8167 (mt) REVERT: F 121 LYS cc_start: 0.7879 (tptp) cc_final: 0.7610 (tptp) outliers start: 107 outliers final: 91 residues processed: 646 average time/residue: 0.3479 time to fit residues: 336.8752 Evaluate side-chains 684 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 585 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 0.8980 chunk 256 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 33 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS C 184 HIS ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS F 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21945 Z= 0.233 Angle : 0.703 13.618 29790 Z= 0.359 Chirality : 0.046 0.339 3309 Planarity : 0.005 0.059 3876 Dihedral : 5.490 57.737 3009 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 3.24 % Allowed : 19.66 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % 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: -1.66 (0.15), residues: 2754 helix: -0.38 (0.26), residues: 372 sheet: -0.53 (0.18), residues: 810 loop : -1.62 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP F 14 HIS 0.026 0.002 HIS C 75 PHE 0.030 0.002 PHE H 27 TYR 0.017 0.001 TYR L 173 ARG 0.010 0.001 ARG C 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 583 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 GLN cc_start: 0.5818 (mp-120) cc_final: 0.5448 (mm-40) REVERT: I 68 PHE cc_start: 0.7565 (m-80) cc_final: 0.7103 (m-80) REVERT: I 83 MET cc_start: 0.5920 (mtp) cc_final: 0.4393 (mtp) REVERT: I 108 TYR cc_start: 0.6056 (m-80) cc_final: 0.5281 (m-80) REVERT: I 117 MET cc_start: 0.6832 (mtm) cc_final: 0.6240 (mtt) REVERT: I 217 HIS cc_start: 0.4860 (t-90) cc_final: 0.3877 (t-90) REVERT: K 11 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8392 (m) REVERT: K 27 GLN cc_start: 0.6610 (pp30) cc_final: 0.6391 (pp30) REVERT: K 71 PHE cc_start: 0.6825 (m-80) cc_final: 0.6623 (m-80) REVERT: K 147 GLN cc_start: 0.6533 (pp30) cc_final: 0.4728 (mp10) REVERT: K 149 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6836 (mmmt) REVERT: K 176 SER cc_start: 0.7898 (t) cc_final: 0.7426 (p) REVERT: K 177 SER cc_start: 0.7434 (t) cc_final: 0.7114 (t) REVERT: A 75 HIS cc_start: 0.6430 (m-70) cc_final: 0.6013 (m-70) REVERT: A 92 LYS cc_start: 0.8798 (pttp) cc_final: 0.8321 (pttp) REVERT: A 109 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7736 (ttp80) REVERT: A 119 GLU cc_start: 0.7562 (tt0) cc_final: 0.6735 (tt0) REVERT: A 121 ILE cc_start: 0.8409 (mp) cc_final: 0.8165 (mm) REVERT: A 125 PHE cc_start: 0.6825 (m-80) cc_final: 0.6504 (m-10) REVERT: A 150 ARG cc_start: 0.7954 (mmm160) cc_final: 0.7191 (mmm-85) REVERT: A 208 ARG cc_start: 0.7323 (mtt90) cc_final: 0.6516 (mtt90) REVERT: A 223 VAL cc_start: 0.7284 (t) cc_final: 0.7048 (p) REVERT: A 233 TYR cc_start: 0.6599 (m-80) cc_final: 0.5997 (m-80) REVERT: A 260 MET cc_start: 0.6890 (mmm) cc_final: 0.6630 (mpp) REVERT: A 275 ASP cc_start: 0.7021 (t0) cc_final: 0.6736 (t0) REVERT: B 79 ASP cc_start: 0.7267 (m-30) cc_final: 0.6902 (m-30) REVERT: B 91 LEU cc_start: 0.7552 (mt) cc_final: 0.6968 (mt) REVERT: B 94 TYR cc_start: 0.8380 (t80) cc_final: 0.7683 (t80) REVERT: B 95 ASN cc_start: 0.7986 (m110) cc_final: 0.7750 (m110) REVERT: B 115 MET cc_start: 0.6242 (tpp) cc_final: 0.5915 (tpp) REVERT: B 121 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7469 (tptp) REVERT: G 3 GLN cc_start: 0.6202 (mp-120) cc_final: 0.5552 (mp10) REVERT: G 68 PHE cc_start: 0.7442 (m-80) cc_final: 0.6844 (m-80) REVERT: G 83 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.4457 (mtp) REVERT: G 104 SER cc_start: 0.8322 (t) cc_final: 0.7994 (t) REVERT: J 11 VAL cc_start: 0.8720 (p) cc_final: 0.8473 (m) REVERT: J 12 SER cc_start: 0.8239 (m) cc_final: 0.7740 (t) REVERT: J 46 LEU cc_start: 0.5062 (tp) cc_final: 0.4618 (tp) REVERT: J 65 SER cc_start: 0.8096 (t) cc_final: 0.7642 (m) REVERT: J 123 GLU cc_start: 0.5722 (mp0) cc_final: 0.5433 (mp0) REVERT: J 189 HIS cc_start: 0.8116 (m-70) cc_final: 0.7771 (m-70) REVERT: C 71 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 96 ASN cc_start: 0.7963 (t0) cc_final: 0.7214 (t0) REVERT: C 104 ASP cc_start: 0.7618 (m-30) cc_final: 0.7402 (m-30) REVERT: C 109 ARG cc_start: 0.7445 (ttp-170) cc_final: 0.7107 (ttt-90) REVERT: C 120 PHE cc_start: 0.7309 (t80) cc_final: 0.7023 (t80) REVERT: C 132 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8142 (tp-100) REVERT: C 161 TYR cc_start: 0.7412 (t80) cc_final: 0.7137 (t80) REVERT: C 164 LEU cc_start: 0.7038 (mt) cc_final: 0.6811 (mp) REVERT: C 189 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7196 (mm-40) REVERT: C 259 LYS cc_start: 0.7694 (mttt) cc_final: 0.7172 (mtmm) REVERT: C 315 LYS cc_start: 0.7355 (mmtt) cc_final: 0.7046 (mmtt) REVERT: E 17 MET cc_start: 0.3867 (mmm) cc_final: 0.3401 (mmt) REVERT: E 42 GLN cc_start: 0.7502 (tp40) cc_final: 0.7264 (tp-100) REVERT: E 65 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6763 (mm-40) REVERT: E 79 ASP cc_start: 0.7568 (m-30) cc_final: 0.7217 (m-30) REVERT: E 85 GLU cc_start: 0.7044 (tp30) cc_final: 0.6788 (tp30) REVERT: E 91 LEU cc_start: 0.7482 (mt) cc_final: 0.7000 (mt) REVERT: E 95 ASN cc_start: 0.7994 (m-40) cc_final: 0.7512 (m-40) REVERT: E 110 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7275 (tt) REVERT: E 121 LYS cc_start: 0.7619 (tptp) cc_final: 0.7378 (tptp) REVERT: E 163 ARG cc_start: 0.6722 (ttt180) cc_final: 0.6401 (ttt180) REVERT: H 3 GLN cc_start: 0.6300 (mp10) cc_final: 0.5635 (mp10) REVERT: H 65 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8374 (tppp) REVERT: H 70 ILE cc_start: 0.7646 (tp) cc_final: 0.7368 (tp) REVERT: H 117 MET cc_start: 0.6964 (mtm) cc_final: 0.6548 (mtm) REVERT: L 6 GLN cc_start: 0.7245 (mm-40) cc_final: 0.7034 (mm-40) REVERT: L 18 ARG cc_start: 0.7500 (ttm170) cc_final: 0.7245 (ttm170) REVERT: L 20 THR cc_start: 0.8628 (m) cc_final: 0.8375 (p) REVERT: L 74 THR cc_start: 0.7814 (m) cc_final: 0.7433 (p) REVERT: L 176 SER cc_start: 0.7074 (t) cc_final: 0.6710 (p) REVERT: D 57 ARG cc_start: 0.7909 (ttt90) cc_final: 0.7471 (ttm-80) REVERT: D 67 ILE cc_start: 0.7724 (mm) cc_final: 0.7235 (tp) REVERT: D 82 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6332 (mp0) REVERT: D 119 GLU cc_start: 0.7644 (tt0) cc_final: 0.7286 (tt0) REVERT: D 150 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7546 (mmm160) REVERT: D 186 SER cc_start: 0.7857 (p) cc_final: 0.7494 (m) REVERT: D 197 GLN cc_start: 0.7678 (pt0) cc_final: 0.7205 (pm20) REVERT: D 212 THR cc_start: 0.8315 (m) cc_final: 0.8048 (p) REVERT: F 25 ARG cc_start: 0.7018 (tmt170) cc_final: 0.6717 (tmt170) REVERT: F 42 GLN cc_start: 0.7628 (tp40) cc_final: 0.7421 (tp-100) REVERT: F 51 LYS cc_start: 0.7888 (mttt) cc_final: 0.7579 (mptt) REVERT: F 81 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: F 85 GLU cc_start: 0.6805 (tp30) cc_final: 0.6306 (tp30) REVERT: F 89 ILE cc_start: 0.8356 (mt) cc_final: 0.7888 (mt) outliers start: 78 outliers final: 65 residues processed: 621 average time/residue: 0.3529 time to fit residues: 327.0988 Evaluate side-chains 643 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 571 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 172 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 65 GLN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 157 CYS Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 197 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 33 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS C 80 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 290 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.164011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.137312 restraints weight = 36144.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.142768 restraints weight = 17835.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.146355 restraints weight = 10287.302| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 21945 Z= 0.389 Angle : 0.777 12.095 29790 Z= 0.406 Chirality : 0.049 0.332 3309 Planarity : 0.006 0.077 3876 Dihedral : 5.917 57.504 3009 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.84 % Favored : 92.05 % Rotamer: Outliers : 3.99 % Allowed : 19.29 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2754 helix: -0.71 (0.25), residues: 366 sheet: -0.59 (0.18), residues: 813 loop : -1.79 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP F 14 HIS 0.025 0.002 HIS C 75 PHE 0.032 0.002 PHE H 27 TYR 0.022 0.002 TYR B 141 ARG 0.014 0.001 ARG C 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5996.77 seconds wall clock time: 108 minutes 18.02 seconds (6498.02 seconds total)