Starting phenix.real_space_refine on Sat Mar 16 09:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbc_27279/03_2024/8dbc_27279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbc_27279/03_2024/8dbc_27279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbc_27279/03_2024/8dbc_27279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbc_27279/03_2024/8dbc_27279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbc_27279/03_2024/8dbc_27279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbc_27279/03_2024/8dbc_27279.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.203 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 102 5.16 5 C 8892 2.51 5 N 2490 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14232 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 318 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 306 not shown) Time building chain proxies: 6.93, per 1000 atoms: 0.49 Number of scatterers: 14232 At special positions: 0 Unit cell: (122.515, 129.385, 79.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 P 12 15.00 O 2736 8.00 N 2490 7.00 C 8892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.6 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 44.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER B 314 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER C 314 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER D 314 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER F 314 " --> pdb=" O TYR F 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.666A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER E 314 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.215A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.746A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.216A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.745A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1998 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: 4.15 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4557 1.33 - 1.45: 1649 1.45 - 1.57: 8074 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14430 Sorted by residual: bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O4 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O2 PO4 F 402 " pdb=" P PO4 F 402 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O2 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 14425 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 354 106.74 - 113.57: 8439 113.57 - 120.40: 5233 120.40 - 127.22: 5378 127.22 - 134.05: 120 Bond angle restraints: 19524 Sorted by residual: angle pdb=" C LEU B 27 " pdb=" N GLY B 28 " pdb=" CA GLY B 28 " ideal model delta sigma weight residual 120.10 115.71 4.39 9.50e-01 1.11e+00 2.14e+01 angle pdb=" C LEU F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta sigma weight residual 120.10 115.72 4.38 9.50e-01 1.11e+00 2.13e+01 angle pdb=" C LEU A 27 " pdb=" N GLY A 28 " pdb=" CA GLY A 28 " ideal model delta sigma weight residual 120.10 115.73 4.37 9.50e-01 1.11e+00 2.12e+01 angle pdb=" C LEU E 27 " pdb=" N GLY E 28 " pdb=" CA GLY E 28 " ideal model delta sigma weight residual 120.10 115.73 4.37 9.50e-01 1.11e+00 2.12e+01 angle pdb=" C LEU C 27 " pdb=" N GLY C 28 " pdb=" CA GLY C 28 " ideal model delta sigma weight residual 120.10 115.73 4.37 9.50e-01 1.11e+00 2.12e+01 ... (remaining 19519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 7792 15.95 - 31.90: 716 31.90 - 47.85: 216 47.85 - 63.80: 72 63.80 - 79.75: 24 Dihedral angle restraints: 8820 sinusoidal: 3444 harmonic: 5376 Sorted by residual: dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER C 8 " pdb=" C SER C 8 " pdb=" N GLY C 9 " pdb=" CA GLY C 9 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 8817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1446 0.047 - 0.094: 640 0.094 - 0.141: 170 0.141 - 0.188: 36 0.188 - 0.236: 18 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA LEU C 27 " pdb=" N LEU C 27 " pdb=" C LEU C 27 " pdb=" CB LEU C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU F 27 " pdb=" N LEU F 27 " pdb=" C LEU F 27 " pdb=" CB LEU F 27 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA LEU D 27 " pdb=" N LEU D 27 " pdb=" C LEU D 27 " pdb=" CB LEU D 27 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2307 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 26 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU C 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU C 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU C 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 26 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLU A 26 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU A 26 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU A 27 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 26 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C GLU E 26 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU E 26 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU E 27 " -0.021 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 246 2.68 - 3.23: 13661 3.23 - 3.79: 23503 3.79 - 4.34: 31945 4.34 - 4.90: 51985 Nonbonded interactions: 121340 Sorted by model distance: nonbonded pdb=" OD2 ASP F 101 " pdb=" NZ LYS E 176 " model vdw 2.119 2.520 nonbonded pdb=" O ILE F 6 " pdb=" N GLY F 28 " model vdw 2.218 2.520 nonbonded pdb=" O ILE A 6 " pdb=" N GLY A 28 " model vdw 2.218 2.520 nonbonded pdb=" O ILE D 6 " pdb=" N GLY D 28 " model vdw 2.218 2.520 nonbonded pdb=" O ILE B 6 " pdb=" N GLY B 28 " model vdw 2.218 2.520 ... (remaining 121335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.90 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.240 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 37.380 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 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: 0.020 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.007 0.071 14430 Z= 0.475 Angle : 0.768 5.787 19524 Z= 0.485 Chirality : 0.058 0.236 2310 Planarity : 0.004 0.036 2496 Dihedral : 15.091 79.753 5316 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.74 % Allowed : 13.30 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1830 helix: 1.20 (0.21), residues: 744 sheet: 0.04 (0.25), residues: 474 loop : -0.47 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 162 HIS 0.005 0.002 HIS C 130 PHE 0.011 0.002 PHE C 189 TYR 0.022 0.004 TYR B 146 ARG 0.004 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 419 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8555 (mttp) cc_final: 0.8337 (mttt) REVERT: B 18 LYS cc_start: 0.8651 (mttp) cc_final: 0.8383 (mttt) REVERT: B 78 LYS cc_start: 0.8219 (tptm) cc_final: 0.8019 (tptt) REVERT: B 79 ILE cc_start: 0.8228 (pt) cc_final: 0.7645 (mm) REVERT: B 307 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7534 (mt-10) REVERT: C 3 ASN cc_start: 0.7729 (m-40) cc_final: 0.7319 (m110) REVERT: C 18 LYS cc_start: 0.8684 (mttp) cc_final: 0.8366 (mttt) REVERT: C 307 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7490 (mt-10) REVERT: C 314 SER cc_start: 0.5574 (OUTLIER) cc_final: 0.5212 (p) REVERT: D 3 ASN cc_start: 0.7731 (m-40) cc_final: 0.7355 (m110) REVERT: D 18 LYS cc_start: 0.8676 (mttp) cc_final: 0.8356 (mttt) REVERT: D 307 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7498 (mt-10) REVERT: D 314 SER cc_start: 0.5582 (OUTLIER) cc_final: 0.5222 (p) REVERT: F 220 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6420 (t0) REVERT: F 311 TYR cc_start: 0.5933 (t80) cc_final: 0.5713 (t80) REVERT: E 18 LYS cc_start: 0.8658 (mttp) cc_final: 0.8392 (mttt) REVERT: E 78 LYS cc_start: 0.8291 (tptm) cc_final: 0.8028 (tptt) REVERT: E 79 ILE cc_start: 0.8243 (pt) cc_final: 0.7652 (mm) REVERT: E 307 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7492 (mt-10) outliers start: 43 outliers final: 10 residues processed: 455 average time/residue: 0.3052 time to fit residues: 191.0320 Evaluate side-chains 369 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 356 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 0.0770 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 262 ASN A 263 ASN A 305 ASN B 66 ASN B 123 HIS B 193 HIS B 305 ASN C 64 ASN C 193 HIS C 263 ASN D 64 ASN D 193 HIS D 263 ASN F 64 ASN F 305 ASN E 66 ASN E 123 HIS E 305 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14430 Z= 0.225 Angle : 0.536 7.618 19524 Z= 0.293 Chirality : 0.048 0.172 2310 Planarity : 0.003 0.020 2496 Dihedral : 5.227 45.393 1983 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.99 % Allowed : 13.30 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1830 helix: 1.40 (0.20), residues: 756 sheet: -0.17 (0.23), residues: 498 loop : -0.33 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 162 HIS 0.007 0.001 HIS A 193 PHE 0.016 0.002 PHE D 266 TYR 0.013 0.001 TYR F 146 ARG 0.006 0.001 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 356 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8662 (mttp) cc_final: 0.8454 (mttt) REVERT: A 21 ASP cc_start: 0.7079 (m-30) cc_final: 0.6871 (m-30) REVERT: A 296 LEU cc_start: 0.8898 (mt) cc_final: 0.8631 (mt) REVERT: B 52 ASP cc_start: 0.8287 (t0) cc_final: 0.8057 (m-30) REVERT: B 307 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7528 (mt-10) REVERT: C 247 ILE cc_start: 0.8942 (mt) cc_final: 0.8713 (mt) REVERT: C 307 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7585 (mt-10) REVERT: D 247 ILE cc_start: 0.8954 (mt) cc_final: 0.8716 (mt) REVERT: D 307 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7635 (mt-10) REVERT: F 220 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6735 (t0) REVERT: F 296 LEU cc_start: 0.8632 (mt) cc_final: 0.8428 (mt) REVERT: E 38 GLN cc_start: 0.7473 (mt0) cc_final: 0.7190 (mt0) REVERT: E 52 ASP cc_start: 0.8268 (t0) cc_final: 0.8052 (m-30) REVERT: E 307 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7531 (mt-10) outliers start: 47 outliers final: 22 residues processed: 397 average time/residue: 0.3078 time to fit residues: 168.1175 Evaluate side-chains 349 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 326 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN C 158 ASN D 158 ASN F 12 HIS F 158 ASN E 13 GLN E 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14430 Z= 0.254 Angle : 0.517 5.835 19524 Z= 0.281 Chirality : 0.048 0.171 2310 Planarity : 0.003 0.020 2496 Dihedral : 4.938 41.554 1978 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.82 % Allowed : 12.47 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1830 helix: 1.70 (0.20), residues: 756 sheet: -0.40 (0.22), residues: 510 loop : -0.34 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.005 0.001 HIS B 193 PHE 0.008 0.002 PHE C 138 TYR 0.011 0.002 TYR F 311 ARG 0.006 0.001 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 349 time to evaluate : 1.666 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8845 (mt) cc_final: 0.8606 (mt) REVERT: B 52 ASP cc_start: 0.8328 (t0) cc_final: 0.8056 (m-30) REVERT: B 78 LYS cc_start: 0.8325 (tptt) cc_final: 0.7943 (tptt) REVERT: B 79 ILE cc_start: 0.8307 (pt) cc_final: 0.7857 (mm) REVERT: B 291 ASP cc_start: 0.7375 (t70) cc_final: 0.7162 (t0) REVERT: C 307 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7613 (mt-10) REVERT: D 156 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7367 (mtm-85) REVERT: D 307 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7827 (mt-10) REVERT: F 21 ASP cc_start: 0.6541 (m-30) cc_final: 0.6302 (m-30) REVERT: F 296 LEU cc_start: 0.8814 (mt) cc_final: 0.8606 (mt) REVERT: E 38 GLN cc_start: 0.7323 (mt0) cc_final: 0.7073 (mt0) REVERT: E 52 ASP cc_start: 0.8303 (t0) cc_final: 0.8055 (m-30) REVERT: E 78 LYS cc_start: 0.8322 (tptt) cc_final: 0.7932 (tptt) REVERT: E 79 ILE cc_start: 0.8315 (pt) cc_final: 0.7872 (mm) REVERT: E 291 ASP cc_start: 0.7371 (t70) cc_final: 0.7148 (t0) REVERT: E 307 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7557 (mt-10) outliers start: 60 outliers final: 35 residues processed: 387 average time/residue: 0.3304 time to fit residues: 172.2650 Evaluate side-chains 345 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 310 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 84 optimal weight: 0.0170 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN C 64 ASN C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 158 ASN F 12 HIS E 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14430 Z= 0.218 Angle : 0.490 6.392 19524 Z= 0.267 Chirality : 0.047 0.171 2310 Planarity : 0.003 0.025 2496 Dihedral : 4.416 31.346 1970 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.56 % Allowed : 13.80 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1830 helix: 1.89 (0.20), residues: 756 sheet: -0.45 (0.22), residues: 510 loop : -0.39 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 162 HIS 0.006 0.001 HIS C 193 PHE 0.008 0.001 PHE A 266 TYR 0.013 0.001 TYR F 311 ARG 0.007 0.001 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 330 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8832 (mt) cc_final: 0.8616 (mt) REVERT: B 52 ASP cc_start: 0.8346 (t0) cc_final: 0.8063 (m-30) REVERT: B 78 LYS cc_start: 0.8331 (tptt) cc_final: 0.7955 (tptt) REVERT: B 79 ILE cc_start: 0.8346 (pt) cc_final: 0.7913 (mm) REVERT: C 11 SER cc_start: 0.8315 (p) cc_final: 0.7998 (p) REVERT: C 307 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7627 (mt-10) REVERT: D 11 SER cc_start: 0.8302 (p) cc_final: 0.8002 (p) REVERT: D 307 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7757 (mt-10) REVERT: F 296 LEU cc_start: 0.8791 (mt) cc_final: 0.8583 (mt) REVERT: E 52 ASP cc_start: 0.8340 (t0) cc_final: 0.8111 (m-30) REVERT: E 79 ILE cc_start: 0.8361 (pt) cc_final: 0.7938 (mm) REVERT: E 291 ASP cc_start: 0.7301 (t70) cc_final: 0.7013 (t0) REVERT: E 307 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7625 (mt-10) outliers start: 56 outliers final: 39 residues processed: 366 average time/residue: 0.2966 time to fit residues: 151.0289 Evaluate side-chains 332 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 293 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.0270 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN F 158 ASN E 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14430 Z= 0.199 Angle : 0.476 7.436 19524 Z= 0.258 Chirality : 0.046 0.165 2310 Planarity : 0.003 0.030 2496 Dihedral : 4.307 31.350 1970 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.24 % Allowed : 15.20 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1830 helix: 2.04 (0.20), residues: 756 sheet: -0.57 (0.22), residues: 546 loop : -0.75 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.005 0.001 HIS C 193 PHE 0.031 0.001 PHE A 189 TYR 0.011 0.001 TYR F 311 ARG 0.007 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 298 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.8827 (mt) cc_final: 0.8607 (mt) REVERT: B 52 ASP cc_start: 0.8346 (t0) cc_final: 0.8126 (m-30) REVERT: B 79 ILE cc_start: 0.8289 (pt) cc_final: 0.7913 (mm) REVERT: B 291 ASP cc_start: 0.7131 (t0) cc_final: 0.6851 (t0) REVERT: C 307 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7772 (mt-10) REVERT: D 11 SER cc_start: 0.8266 (p) cc_final: 0.8050 (p) REVERT: D 307 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7771 (mt-10) REVERT: E 52 ASP cc_start: 0.8343 (t0) cc_final: 0.8129 (m-30) REVERT: E 79 ILE cc_start: 0.8306 (pt) cc_final: 0.7933 (mm) REVERT: E 291 ASP cc_start: 0.7293 (t70) cc_final: 0.6950 (t0) REVERT: E 307 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7608 (mt-10) outliers start: 51 outliers final: 36 residues processed: 330 average time/residue: 0.2826 time to fit residues: 131.5850 Evaluate side-chains 312 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 144 optimal weight: 0.0070 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 HIS E 193 HIS E 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14430 Z= 0.198 Angle : 0.473 7.995 19524 Z= 0.255 Chirality : 0.046 0.164 2310 Planarity : 0.003 0.025 2496 Dihedral : 4.238 30.093 1970 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.80 % Allowed : 16.28 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1830 helix: 2.06 (0.20), residues: 756 sheet: -0.59 (0.22), residues: 546 loop : -0.78 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 162 HIS 0.006 0.001 HIS C 193 PHE 0.023 0.001 PHE A 189 TYR 0.010 0.001 TYR F 311 ARG 0.006 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 292 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: B 52 ASP cc_start: 0.8350 (t0) cc_final: 0.8145 (m-30) REVERT: B 79 ILE cc_start: 0.8280 (pt) cc_final: 0.7927 (mm) REVERT: B 291 ASP cc_start: 0.7139 (t0) cc_final: 0.6847 (t0) REVERT: C 279 ASP cc_start: 0.2840 (t0) cc_final: 0.2626 (t0) REVERT: C 307 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 279 ASP cc_start: 0.2855 (t0) cc_final: 0.2623 (t0) REVERT: D 307 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7772 (mt-10) REVERT: F 291 ASP cc_start: 0.7216 (t0) cc_final: 0.6967 (t0) REVERT: E 79 ILE cc_start: 0.8299 (pt) cc_final: 0.7942 (mm) REVERT: E 291 ASP cc_start: 0.7304 (t70) cc_final: 0.6944 (t0) REVERT: E 307 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7618 (mt-10) outliers start: 44 outliers final: 37 residues processed: 317 average time/residue: 0.2801 time to fit residues: 126.1206 Evaluate side-chains 310 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 273 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 99 optimal weight: 0.0030 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 263 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 17 GLN D 158 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14430 Z= 0.177 Angle : 0.463 7.936 19524 Z= 0.248 Chirality : 0.046 0.162 2310 Planarity : 0.003 0.028 2496 Dihedral : 4.055 29.246 1968 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.93 % Allowed : 16.73 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1830 helix: 2.14 (0.20), residues: 756 sheet: -0.52 (0.23), residues: 510 loop : -0.49 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 162 HIS 0.005 0.001 HIS D 193 PHE 0.021 0.001 PHE A 189 TYR 0.009 0.001 TYR F 311 ARG 0.007 0.000 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 283 time to evaluate : 1.628 Fit side-chains revert: symmetry clash REVERT: B 79 ILE cc_start: 0.8263 (pt) cc_final: 0.7962 (mm) REVERT: B 291 ASP cc_start: 0.7147 (t0) cc_final: 0.6855 (t0) REVERT: C 279 ASP cc_start: 0.2823 (t0) cc_final: 0.2617 (t0) REVERT: C 307 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7758 (mt-10) REVERT: D 279 ASP cc_start: 0.2839 (t0) cc_final: 0.2629 (t0) REVERT: D 307 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7762 (mt-10) REVERT: F 265 CYS cc_start: 0.7574 (p) cc_final: 0.7344 (p) REVERT: E 79 ILE cc_start: 0.8285 (pt) cc_final: 0.7985 (mm) REVERT: E 99 LYS cc_start: 0.7509 (pttm) cc_final: 0.7272 (pttp) REVERT: E 291 ASP cc_start: 0.7299 (t70) cc_final: 0.6931 (t0) REVERT: E 307 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7633 (mt-10) outliers start: 46 outliers final: 40 residues processed: 310 average time/residue: 0.2573 time to fit residues: 116.3605 Evaluate side-chains 320 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 280 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 110 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 136 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14430 Z= 0.174 Angle : 0.461 8.472 19524 Z= 0.247 Chirality : 0.046 0.164 2310 Planarity : 0.003 0.030 2496 Dihedral : 4.009 28.419 1968 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.93 % Allowed : 17.37 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1830 helix: 2.17 (0.20), residues: 756 sheet: -0.49 (0.23), residues: 510 loop : -0.53 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 162 HIS 0.005 0.001 HIS D 193 PHE 0.019 0.001 PHE A 189 TYR 0.009 0.001 TYR F 311 ARG 0.008 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 291 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 ILE cc_start: 0.8247 (pt) cc_final: 0.7953 (mm) REVERT: B 291 ASP cc_start: 0.7146 (t0) cc_final: 0.6853 (t0) REVERT: C 307 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7754 (mt-10) REVERT: D 307 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7754 (mt-10) REVERT: F 265 CYS cc_start: 0.7631 (p) cc_final: 0.7389 (p) REVERT: E 79 ILE cc_start: 0.8273 (pt) cc_final: 0.7972 (mm) REVERT: E 99 LYS cc_start: 0.7481 (pttm) cc_final: 0.7257 (pttp) REVERT: E 291 ASP cc_start: 0.7299 (t70) cc_final: 0.6915 (t0) REVERT: E 307 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7630 (mt-10) outliers start: 46 outliers final: 42 residues processed: 319 average time/residue: 0.2685 time to fit residues: 122.1402 Evaluate side-chains 316 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 274 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 222 MET Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.3980 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 146 optimal weight: 0.0770 chunk 152 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 263 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14430 Z= 0.151 Angle : 0.459 8.908 19524 Z= 0.244 Chirality : 0.045 0.159 2310 Planarity : 0.003 0.030 2496 Dihedral : 3.934 28.059 1968 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.99 % Allowed : 17.43 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1830 helix: 2.24 (0.20), residues: 756 sheet: -0.46 (0.23), residues: 510 loop : -0.53 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 162 HIS 0.005 0.001 HIS D 193 PHE 0.018 0.001 PHE A 189 TYR 0.008 0.001 TYR F 311 ARG 0.008 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 290 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 ILE cc_start: 0.8219 (pt) cc_final: 0.7958 (mm) REVERT: B 291 ASP cc_start: 0.7093 (t0) cc_final: 0.6789 (t0) REVERT: C 307 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7739 (mt-10) REVERT: D 307 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7827 (mt-10) REVERT: E 79 ILE cc_start: 0.8246 (pt) cc_final: 0.7977 (mm) REVERT: E 291 ASP cc_start: 0.7309 (t70) cc_final: 0.6937 (t0) REVERT: E 307 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7615 (mt-10) outliers start: 47 outliers final: 39 residues processed: 317 average time/residue: 0.2844 time to fit residues: 127.6892 Evaluate side-chains 314 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 275 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN C 158 ASN ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14430 Z= 0.208 Angle : 0.483 9.513 19524 Z= 0.257 Chirality : 0.046 0.182 2310 Planarity : 0.003 0.033 2496 Dihedral : 3.948 27.421 1966 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.86 % Allowed : 17.56 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1830 helix: 2.13 (0.20), residues: 756 sheet: -0.48 (0.23), residues: 510 loop : -0.57 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 162 HIS 0.006 0.001 HIS D 193 PHE 0.018 0.001 PHE A 189 TYR 0.008 0.001 TYR F 311 ARG 0.007 0.001 ARG C 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 292 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 ILE cc_start: 0.8266 (pt) cc_final: 0.7951 (mm) REVERT: B 291 ASP cc_start: 0.7135 (t0) cc_final: 0.6837 (t0) REVERT: C 307 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7761 (mt-10) REVERT: D 307 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7787 (mt-10) REVERT: E 79 ILE cc_start: 0.8283 (pt) cc_final: 0.7965 (mm) REVERT: E 291 ASP cc_start: 0.7325 (t70) cc_final: 0.6969 (t0) REVERT: E 307 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7599 (mt-10) outliers start: 45 outliers final: 42 residues processed: 318 average time/residue: 0.2714 time to fit residues: 123.1197 Evaluate side-chains 325 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 283 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 222 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 143 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 263 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.172116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.132101 restraints weight = 14771.234| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.59 r_work: 0.3149 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14430 Z= 0.162 Angle : 0.467 9.276 19524 Z= 0.248 Chirality : 0.045 0.160 2310 Planarity : 0.003 0.030 2496 Dihedral : 3.771 27.348 1964 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.93 % Allowed : 17.88 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1830 helix: 2.21 (0.20), residues: 756 sheet: -0.44 (0.23), residues: 510 loop : -0.52 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.005 0.001 HIS C 193 PHE 0.017 0.001 PHE A 189 TYR 0.008 0.001 TYR F 311 ARG 0.007 0.001 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.97 seconds wall clock time: 65 minutes 32.79 seconds (3932.79 seconds total)