Starting phenix.real_space_refine on Sat Jan 20 06:20:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/01_2024/7yox_33989.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/01_2024/7yox_33989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/01_2024/7yox_33989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/01_2024/7yox_33989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/01_2024/7yox_33989.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yox_33989/01_2024/7yox_33989.pdb" } resolution = 3.95 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 8745 2.51 5 N 2355 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 327": "OD1" <-> "OD2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "E ASP 4": "OD1" <-> "OD2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 287": "OD1" <-> "OD2" Residue "F ASP 300": "OD1" <-> "OD2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F ASP 349": "OD1" <-> "OD2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "C" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "E" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "F" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Time building chain proxies: 7.69, per 1000 atoms: 0.55 Number of scatterers: 13878 At special positions: 0 Unit cell: (77.738, 138.109, 143.071, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2676 8.00 N 2355 7.00 C 8745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 172 " distance=2.54 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 172 " distance=2.03 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS F 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 2.8 seconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3342 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 17 sheets defined 33.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.901A pdb=" N LYS A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.639A pdb=" N THR A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.537A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'B' and resid 2 through 21 Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 61 through 84 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.761A pdb=" N GLU C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 179 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'D' and resid 2 through 31 removed outlier: 3.763A pdb=" N LYS D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 51 through 61 removed outlier: 3.548A pdb=" N GLY D 55 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 84 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'E' and resid 3 through 26 removed outlier: 4.544A pdb=" N GLU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR E 20 " --> pdb=" O TYR E 16 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN E 23 " --> pdb=" O GLU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 61 through 83 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.811A pdb=" N THR E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 90 through 108 removed outlier: 4.092A pdb=" N GLU F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.704A pdb=" N THR F 135 " --> pdb=" O GLY F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 148 Processing helix chain 'F' and resid 148 through 179 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 318 through 320 No H-bonds generated for 'chain 'F' and resid 318 through 320' Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 365 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 124 removed outlier: 5.686A pdb=" N ILE A 121 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A 199 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 123 " --> pdb=" O TYR A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 228 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 218 through 228 current: chain 'A' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 248 through 252 current: chain 'A' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 310 through 316 current: chain 'A' and resid 352 through 364 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 43 removed outlier: 6.784A pdb=" N TYR B 38 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG B 99 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 40 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER B 101 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 42 " --> pdb=" O SER B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 140 removed outlier: 3.546A pdb=" N GLN B 200 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 12.901A pdb=" N SER B 219 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE B 261 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 221 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 241 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 268 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B 239 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL B 130 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 205 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 132 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 143 Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA7, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.017A pdb=" N ILE C 121 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C 199 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 123 " --> pdb=" O TYR C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 205 removed outlier: 3.873A pdb=" N ARG C 222 " --> pdb=" O THR C 205 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 218 through 225 current: chain 'C' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 248 through 252 current: chain 'C' and resid 310 through 315 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 310 through 315 current: chain 'C' and resid 356 through 363 Processing sheet with id=AA9, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 43 removed outlier: 5.483A pdb=" N TYR D 38 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG D 99 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 40 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER D 101 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D 42 " --> pdb=" O SER D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 123 through 133 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 123 through 133 current: chain 'D' and resid 196 through 205 removed outlier: 3.605A pdb=" N GLN D 200 " --> pdb=" O LEU D 224 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 219 through 225 current: chain 'D' and resid 259 through 264 Processing sheet with id=AB3, first strand: chain 'D' and resid 142 through 147 removed outlier: 3.605A pdb=" N PHE D 154 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS D 147 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 152 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 43 Processing sheet with id=AB5, first strand: chain 'E' and resid 137 through 139 removed outlier: 8.542A pdb=" N SER E 219 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LEU E 263 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA E 265 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE E 223 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR E 267 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLU E 225 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N GLN E 269 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE E 261 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG E 247 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU E 263 " --> pdb=" O MET E 245 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET E 245 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA E 265 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 243 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL E 130 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN E 205 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 132 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 142 through 146 removed outlier: 4.224A pdb=" N ARG E 143 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 156 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 120 through 124 Processing sheet with id=AB8, first strand: chain 'F' and resid 218 through 221 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 218 through 221 current: chain 'F' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 248 through 252 current: chain 'F' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 310 through 316 current: chain 'F' and resid 355 through 358 No H-bonds generated for sheet with id=AB8 434 hydrogen bonds defined for protein. 1254 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: 4.08 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3992 1.33 - 1.45: 1993 1.45 - 1.57: 8001 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 14133 Sorted by residual: bond pdb=" CA GLN D 162 " pdb=" C GLN D 162 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.28e-02 6.10e+03 6.61e+00 bond pdb=" CA ARG E 247 " pdb=" C ARG E 247 " ideal model delta sigma weight residual 1.521 1.492 0.029 1.19e-02 7.06e+03 6.10e+00 bond pdb=" C ASN D 266 " pdb=" O ASN D 266 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.79e+00 bond pdb=" C LEU F 145 " pdb=" O LEU F 145 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.33e+00 bond pdb=" C PHE E 13 " pdb=" O PHE E 13 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.13e+00 ... (remaining 14128 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.68: 345 105.68 - 112.76: 7192 112.76 - 119.84: 5071 119.84 - 126.91: 6383 126.91 - 133.99: 122 Bond angle restraints: 19113 Sorted by residual: angle pdb=" N GLN D 162 " pdb=" CA GLN D 162 " pdb=" C GLN D 162 " ideal model delta sigma weight residual 112.26 98.92 13.34 1.32e+00 5.74e-01 1.02e+02 angle pdb=" N CYS D 106 " pdb=" CA CYS D 106 " pdb=" C CYS D 106 " ideal model delta sigma weight residual 108.22 101.45 6.77 9.00e-01 1.23e+00 5.65e+01 angle pdb=" N GLY C 132 " pdb=" CA GLY C 132 " pdb=" C GLY C 132 " ideal model delta sigma weight residual 112.73 120.80 -8.07 1.20e+00 6.94e-01 4.52e+01 angle pdb=" N TYR B 20 " pdb=" CA TYR B 20 " pdb=" C TYR B 20 " ideal model delta sigma weight residual 111.36 118.63 -7.27 1.09e+00 8.42e-01 4.44e+01 angle pdb=" N ILE A 93 " pdb=" CA ILE A 93 " pdb=" C ILE A 93 " ideal model delta sigma weight residual 110.62 117.15 -6.53 1.02e+00 9.61e-01 4.10e+01 ... (remaining 19108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6568 17.90 - 35.81: 932 35.81 - 53.71: 846 53.71 - 71.61: 334 71.61 - 89.51: 41 Dihedral angle restraints: 8721 sinusoidal: 3573 harmonic: 5148 Sorted by residual: dihedral pdb=" CB CYS F 242 " pdb=" SG CYS F 242 " pdb=" SG CYS F 245 " pdb=" CB CYS F 245 " ideal model delta sinusoidal sigma weight residual 93.00 166.91 -73.91 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" C VAL B 155 " pdb=" N VAL B 155 " pdb=" CA VAL B 155 " pdb=" CB VAL B 155 " ideal model delta harmonic sigma weight residual -122.00 -137.57 15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" C PHE C 72 " pdb=" N PHE C 72 " pdb=" CA PHE C 72 " pdb=" CB PHE C 72 " ideal model delta harmonic sigma weight residual -122.60 -137.66 15.06 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 8718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1745 0.112 - 0.224: 364 0.224 - 0.335: 54 0.335 - 0.447: 12 0.447 - 0.559: 3 Chirality restraints: 2178 Sorted by residual: chirality pdb=" CA PHE C 72 " pdb=" N PHE C 72 " pdb=" C PHE C 72 " pdb=" CB PHE C 72 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CA VAL B 155 " pdb=" N VAL B 155 " pdb=" C VAL B 155 " pdb=" CB VAL B 155 " both_signs ideal model delta sigma weight residual False 2.44 1.96 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA GLU F 202 " pdb=" N GLU F 202 " pdb=" C GLU F 202 " pdb=" CB GLU F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 2175 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO B 39 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 249 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.17e+00 pdb=" N PRO D 250 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 250 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 250 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 168 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO D 169 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " 0.039 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.61: 22 1.61 - 2.43: 136 2.43 - 3.25: 14381 3.25 - 4.08: 42455 4.08 - 4.90: 68604 Warning: very small nonbonded interaction distances. Nonbonded interactions: 125598 Sorted by model distance: nonbonded pdb=" O ILE E 28 " pdb=" CB SER E 91 " model vdw 0.786 3.440 nonbonded pdb=" C ILE E 28 " pdb=" CB SER E 91 " model vdw 0.870 3.670 nonbonded pdb=" CA SER E 18 " pdb=" CE1 HIS E 21 " model vdw 0.903 3.690 nonbonded pdb=" O ILE E 28 " pdb=" OG SER E 91 " model vdw 0.918 2.440 nonbonded pdb=" O LEU B 78 " pdb=" OE1 GLN B 82 " model vdw 0.982 3.040 ... (remaining 125593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.350 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 40.820 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.006 0.033 14133 Z= 0.418 Angle : 1.308 13.338 19113 Z= 0.894 Chirality : 0.095 0.559 2178 Planarity : 0.007 0.074 2466 Dihedral : 27.063 89.513 5367 Min Nonbonded Distance : 0.786 Molprobity Statistics. All-atom Clashscore : 33.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.04 % Favored : 98.79 % Rotamer: Outliers : 46.70 % Allowed : 16.89 % Favored : 36.41 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.19), residues: 1737 helix: 3.80 (0.20), residues: 518 sheet: 1.37 (0.25), residues: 426 loop : 0.97 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP F 288 HIS 0.005 0.001 HIS C 195 PHE 0.031 0.003 PHE C 72 TYR 0.024 0.002 TYR C 86 ARG 0.006 0.001 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 744 poor density : 463 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8393 (pt) REVERT: A 96 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 97 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9117 (tp-100) REVERT: A 112 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7803 (mtpp) REVERT: A 130 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: A 153 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 198 VAL cc_start: 0.6681 (OUTLIER) cc_final: 0.5904 (p) REVERT: A 218 TYR cc_start: 0.7766 (t80) cc_final: 0.7257 (t80) REVERT: A 253 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7408 (mp) REVERT: A 288 TRP cc_start: 0.8075 (t60) cc_final: 0.7191 (t60) REVERT: A 300 ASP cc_start: 0.6352 (OUTLIER) cc_final: 0.6035 (p0) REVERT: A 314 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: A 332 THR cc_start: 0.6681 (p) cc_final: 0.6044 (p) REVERT: B 21 HIS cc_start: 0.7866 (m90) cc_final: 0.7195 (m90) REVERT: B 78 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8663 (tp) REVERT: B 84 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7760 (tp) REVERT: B 92 MET cc_start: 0.7550 (pmm) cc_final: 0.6837 (tmm) REVERT: B 119 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: B 149 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8844 (tptp) REVERT: B 189 LEU cc_start: 0.4581 (OUTLIER) cc_final: 0.4326 (pp) REVERT: B 222 VAL cc_start: 0.8842 (t) cc_final: 0.8133 (t) REVERT: B 239 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8422 (p) REVERT: C 69 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6266 (mt) REVERT: C 78 TRP cc_start: 0.7268 (p-90) cc_final: 0.7032 (p-90) REVERT: C 112 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6836 (mttm) REVERT: C 122 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7941 (pp) REVERT: C 125 PHE cc_start: 0.8112 (t80) cc_final: 0.7910 (t80) REVERT: C 152 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8845 (p) REVERT: C 163 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8268 (t) REVERT: C 187 THR cc_start: 0.4795 (OUTLIER) cc_final: 0.4265 (p) REVERT: C 258 TYR cc_start: 0.7116 (t80) cc_final: 0.6761 (t80) REVERT: C 317 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7697 (t70) REVERT: C 353 PHE cc_start: 0.8352 (m-80) cc_final: 0.8128 (m-80) REVERT: C 361 SER cc_start: 0.7776 (OUTLIER) cc_final: 0.7408 (m) REVERT: C 363 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8472 (p) REVERT: D 124 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7911 (pp) REVERT: D 143 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5532 (tpt-90) REVERT: D 145 TYR cc_start: 0.6036 (m-80) cc_final: 0.5544 (m-10) REVERT: D 163 TYR cc_start: 0.7387 (m-10) cc_final: 0.6955 (m-10) REVERT: D 172 CYS cc_start: 0.3736 (OUTLIER) cc_final: 0.1764 (t) REVERT: D 183 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: D 194 THR cc_start: 0.2664 (OUTLIER) cc_final: 0.2154 (t) REVERT: D 254 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8340 (t0) REVERT: E 26 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8294 (pp) REVERT: E 92 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4853 (pmm) REVERT: E 100 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8306 (pp) REVERT: E 120 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8527 (p) REVERT: E 206 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: E 261 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7881 (mt) REVERT: F 63 GLN cc_start: 0.0850 (OUTLIER) cc_final: -0.2429 (tp-100) REVERT: F 65 MET cc_start: 0.1756 (OUTLIER) cc_final: 0.1378 (pmm) REVERT: F 66 GLN cc_start: 0.0813 (OUTLIER) cc_final: 0.0339 (pt0) REVERT: F 69 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.4469 (mm) REVERT: F 78 TRP cc_start: 0.1562 (t-100) cc_final: 0.0667 (t-100) REVERT: F 85 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7843 (p) REVERT: F 93 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8447 (pt) REVERT: F 102 PHE cc_start: 0.8890 (t80) cc_final: 0.8583 (t80) REVERT: F 167 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7050 (t0) REVERT: F 270 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6888 (ptp90) REVERT: F 282 LEU cc_start: 0.9057 (mp) cc_final: 0.8704 (tp) REVERT: F 289 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: F 290 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8032 (t) outliers start: 744 outliers final: 179 residues processed: 980 average time/residue: 0.2949 time to fit residues: 395.7888 Evaluate side-chains 515 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 289 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 270 ARG Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 289 GLN Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 352 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 51 optimal weight: 30.0000 chunk 81 optimal weight: 0.0020 chunk 99 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 overall best weight: 3.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 317 HIS A 339 ASN A 360 ASN B 11 GLN B 43 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS C 136 ASN D 2 ASN D 59 ASN D 82 GLN D 266 ASN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN E 272 ASN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 GLN F 346 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14133 Z= 0.309 Angle : 0.791 11.528 19113 Z= 0.415 Chirality : 0.049 0.336 2178 Planarity : 0.006 0.094 2466 Dihedral : 16.003 86.862 2369 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 29.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 14.56 % Allowed : 29.50 % Favored : 55.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 1737 helix: 1.69 (0.21), residues: 520 sheet: 0.86 (0.26), residues: 393 loop : 0.76 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 248 HIS 0.017 0.002 HIS B 37 PHE 0.042 0.003 PHE D 69 TYR 0.025 0.003 TYR F 201 ARG 0.012 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 266 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8266 (mppt) REVERT: A 194 ILE cc_start: 0.6932 (tp) cc_final: 0.6593 (tp) REVERT: A 198 VAL cc_start: 0.6709 (OUTLIER) cc_final: 0.5978 (p) REVERT: A 218 TYR cc_start: 0.7694 (t80) cc_final: 0.7318 (t80) REVERT: A 332 THR cc_start: 0.6495 (p) cc_final: 0.6028 (p) REVERT: B 21 HIS cc_start: 0.7901 (m90) cc_final: 0.7107 (m90) REVERT: B 28 ILE cc_start: 0.8743 (mm) cc_final: 0.8254 (mm) REVERT: B 31 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6361 (mm-30) REVERT: B 48 PHE cc_start: 0.8265 (m-80) cc_final: 0.7781 (m-80) REVERT: B 69 PHE cc_start: 0.8668 (m-10) cc_final: 0.8361 (m-80) REVERT: B 84 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7906 (tp) REVERT: B 92 MET cc_start: 0.7538 (pmm) cc_final: 0.7048 (tmm) REVERT: B 124 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 149 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8583 (tptp) REVERT: B 163 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: B 222 VAL cc_start: 0.9032 (t) cc_final: 0.8702 (t) REVERT: B 260 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7462 (mp0) REVERT: C 65 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6567 (ppp) REVERT: C 71 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7834 (tpp-160) REVERT: C 78 TRP cc_start: 0.7415 (p-90) cc_final: 0.7101 (p-90) REVERT: C 164 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9270 (tm) REVERT: D 146 MET cc_start: 0.7515 (tmm) cc_final: 0.6954 (tmm) REVERT: E 157 LYS cc_start: 0.7588 (mmtm) cc_final: 0.6732 (ttpt) REVERT: E 225 GLU cc_start: 0.8158 (tp30) cc_final: 0.7658 (mm-30) REVERT: E 241 TYR cc_start: 0.8223 (m-10) cc_final: 0.7949 (m-10) REVERT: F 85 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8031 (p) REVERT: F 95 LYS cc_start: 0.9370 (mtmp) cc_final: 0.9013 (mttm) REVERT: F 146 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8518 (mtm-85) REVERT: F 238 MET cc_start: 0.8091 (tpp) cc_final: 0.7862 (tpp) REVERT: F 282 LEU cc_start: 0.9048 (mp) cc_final: 0.8670 (tp) REVERT: F 289 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: F 314 GLU cc_start: 0.8579 (mp0) cc_final: 0.8144 (mp0) outliers start: 232 outliers final: 136 residues processed: 448 average time/residue: 0.2602 time to fit residues: 170.7039 Evaluate side-chains 358 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 209 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 289 GLN Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 124 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 207 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS C 136 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 266 ASN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN E 148 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN E 253 GLN ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 14133 Z= 0.444 Angle : 0.809 12.546 19113 Z= 0.437 Chirality : 0.049 0.282 2178 Planarity : 0.006 0.077 2466 Dihedral : 12.516 82.950 2096 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 38.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 13.81 % Allowed : 29.57 % Favored : 56.62 % 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: 0.58 (0.20), residues: 1737 helix: 0.82 (0.22), residues: 513 sheet: 0.24 (0.26), residues: 394 loop : 0.36 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP D 248 HIS 0.034 0.002 HIS A 193 PHE 0.036 0.004 PHE D 69 TYR 0.032 0.003 TYR B 164 ARG 0.011 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 207 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7428 (ttpt) REVERT: A 118 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6589 (ttpp) REVERT: A 195 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.6824 (p90) REVERT: A 217 LYS cc_start: 0.6435 (OUTLIER) cc_final: 0.6156 (mtmm) REVERT: B 28 ILE cc_start: 0.8876 (mm) cc_final: 0.8472 (mm) REVERT: B 31 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5781 (mm-30) REVERT: B 32 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7019 (ptp90) REVERT: B 69 PHE cc_start: 0.8879 (m-10) cc_final: 0.8656 (m-80) REVERT: B 92 MET cc_start: 0.7393 (pmm) cc_final: 0.6657 (ppp) REVERT: B 139 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8086 (mm) REVERT: B 149 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8481 (tptp) REVERT: B 164 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7720 (t80) REVERT: B 189 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.4339 (pp) REVERT: C 65 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6764 (ppp) REVERT: C 164 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9187 (tm) REVERT: C 247 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6985 (mm-30) REVERT: C 314 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7654 (mp0) REVERT: D 237 ASP cc_start: 0.8223 (m-30) cc_final: 0.7997 (m-30) REVERT: D 254 ASP cc_start: 0.8774 (t0) cc_final: 0.8559 (t0) REVERT: D 274 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7475 (mm-40) REVERT: E 187 SER cc_start: 0.4655 (OUTLIER) cc_final: 0.4310 (t) REVERT: E 207 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7909 (mm110) REVERT: E 220 MET cc_start: 0.7825 (mmm) cc_final: 0.7100 (mmm) REVERT: E 241 TYR cc_start: 0.8379 (m-10) cc_final: 0.8104 (m-10) REVERT: F 63 GLN cc_start: -0.0212 (OUTLIER) cc_final: -0.3299 (tp40) REVERT: F 65 MET cc_start: 0.3471 (ptp) cc_final: 0.2860 (pmm) REVERT: F 69 LEU cc_start: 0.5596 (OUTLIER) cc_final: 0.5268 (mp) REVERT: F 85 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8027 (p) REVERT: F 146 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8504 (mtm-85) REVERT: F 197 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7624 (mtm180) REVERT: F 238 MET cc_start: 0.7934 (tpp) cc_final: 0.7727 (tpp) outliers start: 220 outliers final: 155 residues processed: 394 average time/residue: 0.2403 time to fit residues: 138.8063 Evaluate side-chains 356 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 181 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 154 PHE Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 197 ARG Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 365 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 0.0770 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 81 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 overall best weight: 3.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6327 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: