Starting phenix.real_space_refine on Sun Feb 18 03:41:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6h_14527/02_2024/7z6h_14527_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6h_14527/02_2024/7z6h_14527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6h_14527/02_2024/7z6h_14527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6h_14527/02_2024/7z6h_14527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6h_14527/02_2024/7z6h_14527_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6h_14527/02_2024/7z6h_14527_updated.pdb" } resolution = 3.59 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= 0.003 sd= 0.039 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 46 5.49 5 S 137 5.16 5 C 12953 2.51 5 N 3561 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 175": "OD1" <-> "OD2" Residue "G PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 219": "OD1" <-> "OD2" Residue "K GLU 279": "OE1" <-> "OE2" Residue "K GLU 323": "OE1" <-> "OE2" Residue "K ASP 332": "OD1" <-> "OD2" Residue "K PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20629 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1911 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 4 Chain: "B" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2049 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 250} Chain: "C" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2171 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 2 Chain: "D" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2499 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2671 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2480 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 12, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2523 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 304} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3518 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 23, 'TRANS': 414} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "Y" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 198 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.41, per 1000 atoms: 0.55 Number of scatterers: 20629 At special positions: 0 Unit cell: (146.2, 117.82, 130.72, 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 137 16.00 P 46 15.00 O 3932 8.00 N 3561 7.00 C 12953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 272 " 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.03 Conformation dependent library (CDL) restraints added in 3.9 seconds 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 17 sheets defined 42.9% alpha, 12.4% beta 0 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 8.06 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.914A pdb=" N ILE B 34 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 161 through 170 removed outlier: 4.860A pdb=" N GLU B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Proline residue: B 230 - end of helix removed outlier: 5.477A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 26 Processing helix chain 'C' and resid 85 through 95 removed outlier: 3.958A pdb=" N THR C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 146 removed outlier: 4.594A pdb=" N LYS C 144 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 146 " --> pdb=" O TRP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'D' and resid 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 56 through 66 Processing helix chain 'D' and resid 85 through 95 Processing helix chain 'D' and resid 116 through 127 removed outlier: 4.107A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.651A pdb=" N ALA D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 204 through 218 Processing helix chain 'D' and resid 224 through 234 removed outlier: 3.712A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 266 Processing helix chain 'D' and resid 271 through 282 removed outlier: 3.607A pdb=" N GLY D 276 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.819A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'E' and resid 21 through 32 removed outlier: 4.451A pdb=" N CYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 104 through 117 removed outlier: 4.037A pdb=" N GLN E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 154 Processing helix chain 'E' and resid 173 through 178 removed outlier: 3.554A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 203 removed outlier: 3.790A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 218 Processing helix chain 'E' and resid 223 through 236 Processing helix chain 'E' and resid 250 through 264 removed outlier: 3.596A pdb=" N TYR E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 263 " --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 288 through 302 removed outlier: 4.577A pdb=" N ASN E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'F' and resid 38 through 41 No H-bonds generated for 'chain 'F' and resid 38 through 41' Processing helix chain 'F' and resid 55 through 66 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 143 through 145 No H-bonds generated for 'chain 'F' and resid 143 through 145' Processing helix chain 'F' and resid 148 through 157 removed outlier: 4.510A pdb=" N ARG F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 179 through 184 removed outlier: 4.020A pdb=" N ARG F 184 " --> pdb=" O PRO F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 209 Processing helix chain 'F' and resid 215 through 225 Processing helix chain 'F' and resid 229 through 241 Processing helix chain 'F' and resid 248 through 253 Processing helix chain 'F' and resid 260 through 272 removed outlier: 3.721A pdb=" N ASN F 272 " --> pdb=" O GLN F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 288 removed outlier: 3.933A pdb=" N LYS F 280 " --> pdb=" O ASP F 276 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 304 Processing helix chain 'F' and resid 311 through 329 Processing helix chain 'F' and resid 334 through 348 removed outlier: 3.612A pdb=" N LYS F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 25 No H-bonds generated for 'chain 'G' and resid 22 through 25' Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 39 through 49 Processing helix chain 'G' and resid 66 through 77 Processing helix chain 'G' and resid 99 through 102 No H-bonds generated for 'chain 'G' and resid 99 through 102' Processing helix chain 'G' and resid 104 through 109 Processing helix chain 'G' and resid 127 through 129 No H-bonds generated for 'chain 'G' and resid 127 through 129' Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 179 through 192 Proline residue: G 184 - end of helix Processing helix chain 'G' and resid 199 through 207 Processing helix chain 'G' and resid 213 through 224 removed outlier: 3.786A pdb=" N LEU G 217 " --> pdb=" O ARG G 214 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASN G 218 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE G 219 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU G 220 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN G 224 " --> pdb=" O GLN G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 239 Processing helix chain 'G' and resid 244 through 256 Processing helix chain 'G' and resid 259 through 272 Processing helix chain 'G' and resid 278 through 290 Processing helix chain 'G' and resid 296 through 313 removed outlier: 4.678A pdb=" N SER G 313 " --> pdb=" O GLU G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 335 removed outlier: 3.801A pdb=" N VAL G 331 " --> pdb=" O ALA G 327 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR G 332 " --> pdb=" O ALA G 328 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG G 333 " --> pdb=" O PHE G 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 94 No H-bonds generated for 'chain 'K' and resid 91 through 94' Processing helix chain 'K' and resid 100 through 102 No H-bonds generated for 'chain 'K' and resid 100 through 102' Processing helix chain 'K' and resid 107 through 122 Processing helix chain 'K' and resid 143 through 153 Processing helix chain 'K' and resid 192 through 205 Processing helix chain 'K' and resid 230 through 235 Processing helix chain 'K' and resid 238 through 249 Processing helix chain 'K' and resid 266 through 271 Processing helix chain 'K' and resid 276 through 280 Processing helix chain 'K' and resid 292 through 309 Processing helix chain 'K' and resid 319 through 327 removed outlier: 3.622A pdb=" N GLU K 323 " --> pdb=" O LYS K 319 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU K 324 " --> pdb=" O THR K 320 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS K 326 " --> pdb=" O LEU K 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 343 Processing helix chain 'K' and resid 396 through 405 removed outlier: 3.504A pdb=" N GLY K 401 " --> pdb=" O PHE K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 424 through 426 No H-bonds generated for 'chain 'K' and resid 424 through 426' Processing helix chain 'K' and resid 435 through 441 Processing helix chain 'K' and resid 446 through 456 Processing helix chain 'K' and resid 464 through 479 Processing helix chain 'K' and resid 492 through 505 Processing helix chain 'K' and resid 529 through 546 Processing helix chain 'K' and resid 556 through 559 No H-bonds generated for 'chain 'K' and resid 556 through 559' Processing helix chain 'K' and resid 561 through 566 Processing helix chain 'K' and resid 576 through 583 removed outlier: 3.968A pdb=" N PHE K 580 " --> pdb=" O ALA K 576 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 73 through 76 removed outlier: 5.247A pdb=" N GLU A 26 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 41 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 36 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 206 through 208 removed outlier: 3.583A pdb=" N GLN A 206 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 147 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 214 through 217 removed outlier: 3.837A pdb=" N THR A 167 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.782A pdb=" N GLU B 72 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 17 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 111 " --> pdb=" O MET B 120 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= G, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.982A pdb=" N VAL B 267 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 157 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 212 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 219 through 224 Processing sheet with id= I, first strand: chain 'C' and resid 66 through 70 removed outlier: 4.011A pdb=" N GLU C 66 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N PHE C 3 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C 100 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 133 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 78 through 84 removed outlier: 3.598A pdb=" N LYS C 38 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 53 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 230 through 232 Processing sheet with id= L, first strand: chain 'D' and resid 195 through 199 removed outlier: 3.843A pdb=" N GLY D 78 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 106 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.467A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 70 through 75 Processing sheet with id= O, first strand: chain 'F' and resid 186 through 189 removed outlier: 3.706A pdb=" N ILE F 72 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS F 136 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ALA F 168 " --> pdb=" O LYS F 136 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE F 138 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA F 170 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU F 140 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.668A pdb=" N LEU G 56 " --> pdb=" O PHE G 151 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS G 120 " --> pdb=" O ARG G 150 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N CYS G 152 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL G 122 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE G 154 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU G 124 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 132 through 135 removed outlier: 6.558A pdb=" N LEU K 254 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE K 135 " --> pdb=" O LEU K 254 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE K 256 " --> pdb=" O ILE K 135 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ILE K 255 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE K 223 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE K 257 " --> pdb=" O ILE K 223 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL K 225 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN K 157 " --> pdb=" O ILE K 222 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU K 224 " --> pdb=" O GLN K 157 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN K 159 " --> pdb=" O LEU K 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q 838 hydrogen bonds defined for protein. 2385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 9.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6777 1.36 - 1.51: 5449 1.51 - 1.66: 8624 1.66 - 1.80: 110 1.80 - 1.95: 88 Bond restraints: 21048 Sorted by residual: bond pdb=" CB PRO F 77 " pdb=" CG PRO F 77 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.91e+00 bond pdb=" N PRO F 77 " pdb=" CA PRO F 77 " ideal model delta sigma weight residual 1.465 1.408 0.057 2.03e-02 2.43e+03 7.90e+00 bond pdb=" C LYS B 185 " pdb=" N PRO B 186 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.22e+00 bond pdb=" CG PRO F 77 " pdb=" CD PRO F 77 " ideal model delta sigma weight residual 1.503 1.452 0.051 3.40e-02 8.65e+02 2.26e+00 bond pdb=" CB GLU F 315 " pdb=" CG GLU F 315 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 96.33 - 103.88: 360 103.88 - 111.42: 9523 111.42 - 118.96: 7853 118.96 - 126.50: 10523 126.50 - 134.05: 327 Bond angle restraints: 28586 Sorted by residual: angle pdb=" CA PRO F 77 " pdb=" N PRO F 77 " pdb=" CD PRO F 77 " ideal model delta sigma weight residual 112.00 96.33 15.67 1.40e+00 5.10e-01 1.25e+02 angle pdb=" N PRO G 21 " pdb=" CA PRO G 21 " pdb=" CB PRO G 21 " ideal model delta sigma weight residual 103.25 110.80 -7.55 1.05e+00 9.07e-01 5.18e+01 angle pdb=" N PRO F 77 " pdb=" CD PRO F 77 " pdb=" CG PRO F 77 " ideal model delta sigma weight residual 103.20 96.45 6.75 1.50e+00 4.44e-01 2.02e+01 angle pdb=" N LEU K 394 " pdb=" CA LEU K 394 " pdb=" CB LEU K 394 " ideal model delta sigma weight residual 114.17 109.90 4.27 1.14e+00 7.69e-01 1.40e+01 angle pdb=" N VAL F 45 " pdb=" CA VAL F 45 " pdb=" C VAL F 45 " ideal model delta sigma weight residual 112.96 109.34 3.62 1.00e+00 1.00e+00 1.31e+01 ... (remaining 28581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.47: 11761 30.47 - 60.94: 1049 60.94 - 91.40: 38 91.40 - 121.87: 2 121.87 - 152.34: 1 Dihedral angle restraints: 12851 sinusoidal: 5520 harmonic: 7331 Sorted by residual: dihedral pdb=" CB CYS B 58 " pdb=" SG CYS B 58 " pdb=" SG CYS B 272 " pdb=" CB CYS B 272 " ideal model delta sinusoidal sigma weight residual -86.00 -131.69 45.69 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CA PHE A 58 " pdb=" C PHE A 58 " pdb=" N GLN A 59 " pdb=" CA GLN A 59 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" O1A AGS E 401 " pdb=" O3A AGS E 401 " pdb=" PA AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sinusoidal sigma weight residual -67.73 84.61 -152.34 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 12848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2742 0.051 - 0.103: 491 0.103 - 0.154: 83 0.154 - 0.205: 2 0.205 - 0.257: 2 Chirality restraints: 3320 Sorted by residual: chirality pdb=" CA PRO G 21 " pdb=" N PRO G 21 " pdb=" C PRO G 21 " pdb=" CB PRO G 21 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU K 567 " pdb=" CB LEU K 567 " pdb=" CD1 LEU K 567 " pdb=" CD2 LEU K 567 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO K 420 " pdb=" N PRO K 420 " pdb=" C PRO K 420 " pdb=" CB PRO K 420 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 3317 not shown) Planarity restraints: 3509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 76 " 0.124 5.00e-02 4.00e+02 1.75e-01 4.91e+01 pdb=" N PRO F 77 " -0.302 5.00e-02 4.00e+02 pdb=" CA PRO F 77 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO F 77 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 562 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO K 563 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO K 563 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO K 563 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 185 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO B 186 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 186 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 186 " -0.028 5.00e-02 4.00e+02 ... (remaining 3506 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 158 2.62 - 3.19: 16805 3.19 - 3.76: 29681 3.76 - 4.33: 38214 4.33 - 4.90: 65544 Nonbonded interactions: 150402 Sorted by model distance: nonbonded pdb=" OG SER B 16 " pdb=" O TYR B 112 " model vdw 2.045 2.440 nonbonded pdb=" O PHE G 108 " pdb=" OG1 THR G 111 " model vdw 2.119 2.440 nonbonded pdb=" OH TYR E 60 " pdb=" O PHE E 129 " model vdw 2.183 2.440 nonbonded pdb=" NE2 GLN C 244 " pdb=" OH TYR C 274 " model vdw 2.184 2.520 nonbonded pdb=" OG SER B 231 " pdb=" OH TYR B 255 " model vdw 2.202 2.440 ... (remaining 150397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.480 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 59.860 Find NCS groups from input model: 0.700 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 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 : 0.003 0.141 21048 Z= 0.181 Angle : 0.617 15.668 28586 Z= 0.326 Chirality : 0.040 0.257 3320 Planarity : 0.005 0.175 3509 Dihedral : 19.910 152.340 8068 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.36 % Favored : 93.44 % Rotamer: Outliers : 0.68 % Allowed : 35.48 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.27 (0.18), residues: 2469 helix: 1.27 (0.16), residues: 1112 sheet: -0.24 (0.24), residues: 494 loop : -2.08 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 161 HIS 0.008 0.001 HIS C 262 PHE 0.016 0.001 PHE G 145 TYR 0.015 0.001 TYR A 181 ARG 0.006 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 355 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 193 ARG cc_start: 0.8148 (ptp-110) cc_final: 0.7171 (ptp90) REVERT: F 267 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6148 (mt) REVERT: K 268 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6673 (tm-30) REVERT: K 327 GLN cc_start: 0.7565 (tt0) cc_final: 0.7249 (tt0) outliers start: 15 outliers final: 8 residues processed: 364 average time/residue: 0.4055 time to fit residues: 213.7981 Evaluate side-chains 358 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 349 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 127 LYS Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain K residue 400 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 0.3980 chunk 189 optimal weight: 0.0010 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.0040 chunk 127 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 227 optimal weight: 0.4980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN C 244 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 GLN ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.0403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21048 Z= 0.140 Angle : 0.513 10.115 28586 Z= 0.265 Chirality : 0.039 0.156 3320 Planarity : 0.004 0.089 3509 Dihedral : 13.633 152.165 3143 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.72 % Favored : 93.07 % Rotamer: Outliers : 3.83 % Allowed : 33.27 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.16 (0.18), residues: 2469 helix: 1.34 (0.16), residues: 1120 sheet: -0.13 (0.24), residues: 492 loop : -2.07 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 161 HIS 0.005 0.001 HIS A 259 PHE 0.010 0.001 PHE B 36 TYR 0.017 0.001 TYR E 41 ARG 0.006 0.000 ARG K 334 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 356 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7668 (tmm) cc_final: 0.7319 (tpp) REVERT: B 62 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.7185 (p0) REVERT: C 173 MET cc_start: 0.7107 (tpp) cc_final: 0.6864 (mtt) REVERT: F 40 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: F 349 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6897 (tmt) REVERT: K 268 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6618 (tm-30) REVERT: K 567 LEU cc_start: 0.5365 (OUTLIER) cc_final: 0.5150 (tp) REVERT: K 584 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6449 (mm) outliers start: 85 outliers final: 43 residues processed: 413 average time/residue: 0.3829 time to fit residues: 231.3807 Evaluate side-chains 392 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 344 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 567 LEU Chi-restraints excluded: chain K residue 584 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 245 optimal weight: 0.5980 chunk 202 optimal weight: 0.2980 chunk 225 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 244 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 GLN K 159 GLN K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 GLN ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21048 Z= 0.157 Angle : 0.510 10.253 28586 Z= 0.263 Chirality : 0.039 0.157 3320 Planarity : 0.004 0.068 3509 Dihedral : 13.469 152.356 3127 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.84 % Favored : 92.99 % Rotamer: Outliers : 4.78 % Allowed : 32.46 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.12 (0.18), residues: 2469 helix: 1.35 (0.16), residues: 1120 sheet: -0.11 (0.24), residues: 493 loop : -2.02 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 251 HIS 0.006 0.001 HIS C 262 PHE 0.015 0.001 PHE F 223 TYR 0.012 0.001 TYR C 274 ARG 0.005 0.000 ARG G 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 354 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7662 (tmm) cc_final: 0.7356 (tpp) REVERT: B 62 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.7200 (p0) REVERT: B 264 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6363 (mt) REVERT: C 173 MET cc_start: 0.7177 (tpp) cc_final: 0.6935 (mtt) REVERT: D 124 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.6068 (ttpt) REVERT: D 149 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7657 (pt) REVERT: F 40 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: F 256 ASP cc_start: 0.5834 (t0) cc_final: 0.5569 (t0) REVERT: F 267 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.5984 (mt) REVERT: F 349 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6958 (tmt) REVERT: G 24 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5801 (mp0) REVERT: G 101 ILE cc_start: 0.2793 (OUTLIER) cc_final: 0.2257 (mp) REVERT: G 145 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.5146 (p90) REVERT: K 96 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7743 (ptmm) REVERT: K 268 GLN cc_start: 0.7092 (tm-30) cc_final: 0.6592 (tm-30) REVERT: K 584 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6432 (mm) outliers start: 106 outliers final: 57 residues processed: 421 average time/residue: 0.3720 time to fit residues: 228.9260 Evaluate side-chains 418 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 350 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 480 LEU Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 584 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 9.9990 chunk 170 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN E 313 GLN F 172 ASN K 210 GLN K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21048 Z= 0.219 Angle : 0.549 8.575 28586 Z= 0.284 Chirality : 0.040 0.161 3320 Planarity : 0.004 0.071 3509 Dihedral : 13.559 154.416 3127 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.17 % Favored : 92.63 % Rotamer: Outliers : 5.77 % Allowed : 31.97 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2469 helix: 1.22 (0.16), residues: 1120 sheet: -0.14 (0.24), residues: 495 loop : -2.01 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 529 HIS 0.011 0.001 HIS C 267 PHE 0.023 0.001 PHE B 36 TYR 0.017 0.001 TYR E 41 ARG 0.004 0.000 ARG G 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 361 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.5690 (OUTLIER) cc_final: 0.5410 (p90) REVERT: A 144 MET cc_start: 0.7627 (tmm) cc_final: 0.7363 (tpp) REVERT: B 83 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6652 (ttp80) REVERT: C 54 MET cc_start: 0.7326 (tpp) cc_final: 0.6424 (tpp) REVERT: C 170 VAL cc_start: 0.6701 (OUTLIER) cc_final: 0.5500 (m) REVERT: C 173 MET cc_start: 0.7267 (tpp) cc_final: 0.7020 (mtt) REVERT: D 124 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.6149 (tttt) REVERT: D 149 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7725 (pt) REVERT: E 233 CYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7163 (t) REVERT: F 40 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: F 155 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7273 (ptt180) REVERT: F 267 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6041 (mt) REVERT: F 349 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6926 (tmt) REVERT: G 24 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: G 145 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.4856 (p90) REVERT: G 199 GLU cc_start: 0.6298 (tp30) cc_final: 0.5862 (tp30) REVERT: K 268 GLN cc_start: 0.7139 (tm-30) cc_final: 0.6633 (tm-30) REVERT: K 322 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5545 (mp) outliers start: 128 outliers final: 76 residues processed: 445 average time/residue: 0.3972 time to fit residues: 257.9052 Evaluate side-chains 450 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 361 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 270 LYS Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 441 MET Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 179 optimal weight: 0.0570 chunk 99 optimal weight: 0.9990 chunk 206 optimal weight: 0.0060 chunk 167 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 230 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21048 Z= 0.144 Angle : 0.502 8.195 28586 Z= 0.261 Chirality : 0.039 0.159 3320 Planarity : 0.004 0.064 3509 Dihedral : 13.373 156.680 3127 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.99 % Favored : 93.84 % Rotamer: Outliers : 4.73 % Allowed : 33.00 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.08 (0.18), residues: 2469 helix: 1.36 (0.16), residues: 1120 sheet: -0.12 (0.24), residues: 495 loop : -1.95 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 55 HIS 0.008 0.001 HIS C 267 PHE 0.018 0.001 PHE F 223 TYR 0.013 0.001 TYR A 181 ARG 0.004 0.000 ARG G 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 363 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.5496 (OUTLIER) cc_final: 0.5130 (p90) REVERT: A 144 MET cc_start: 0.7599 (tmm) cc_final: 0.7301 (tpp) REVERT: B 83 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6468 (ttp80) REVERT: B 264 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6335 (mt) REVERT: C 173 MET cc_start: 0.7232 (tpp) cc_final: 0.6982 (mtt) REVERT: C 250 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7297 (tmtp) REVERT: D 124 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.6093 (tttt) REVERT: D 149 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7690 (pt) REVERT: E 233 CYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7078 (t) REVERT: F 267 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.5998 (mt) REVERT: F 349 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6948 (tmt) REVERT: G 24 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5915 (mp0) REVERT: G 145 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.4702 (p90) REVERT: G 199 GLU cc_start: 0.6231 (tp30) cc_final: 0.5798 (tp30) REVERT: K 268 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6593 (tm-30) REVERT: K 322 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5398 (mp) outliers start: 105 outliers final: 67 residues processed: 429 average time/residue: 0.3701 time to fit residues: 232.0252 Evaluate side-chains 435 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 356 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 480 LEU Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 241 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN F 152 GLN F 287 HIS ** K 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21048 Z= 0.223 Angle : 0.551 7.943 28586 Z= 0.284 Chirality : 0.040 0.174 3320 Planarity : 0.004 0.069 3509 Dihedral : 13.448 155.889 3127 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.29 % Favored : 92.51 % Rotamer: Outliers : 5.59 % Allowed : 32.78 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.19 (0.18), residues: 2469 helix: 1.25 (0.16), residues: 1117 sheet: -0.18 (0.24), residues: 497 loop : -1.97 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 529 HIS 0.007 0.001 HIS F 287 PHE 0.023 0.001 PHE B 36 TYR 0.017 0.001 TYR E 41 ARG 0.009 0.000 ARG G 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 363 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.5390 (p90) REVERT: A 144 MET cc_start: 0.7565 (tmm) cc_final: 0.7291 (tpp) REVERT: B 57 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.6175 (tttm) REVERT: B 83 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6542 (ttp80) REVERT: C 170 VAL cc_start: 0.6765 (OUTLIER) cc_final: 0.5542 (m) REVERT: C 173 MET cc_start: 0.7279 (tpp) cc_final: 0.7013 (mtt) REVERT: C 250 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7429 (tmtp) REVERT: D 124 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.6227 (tttt) REVERT: D 149 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7766 (pt) REVERT: D 213 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7569 (t0) REVERT: E 202 LYS cc_start: 0.6985 (tmmt) cc_final: 0.6673 (pttt) REVERT: E 233 CYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7112 (t) REVERT: F 155 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7316 (ptt180) REVERT: F 267 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6032 (mt) REVERT: F 349 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.6946 (tmt) REVERT: G 24 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: G 145 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.4637 (p90) REVERT: K 230 ASN cc_start: 0.6769 (t160) cc_final: 0.6515 (t0) REVERT: K 268 GLN cc_start: 0.7177 (tm-30) cc_final: 0.6656 (tm-30) REVERT: K 322 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5301 (mp) outliers start: 124 outliers final: 85 residues processed: 441 average time/residue: 0.3661 time to fit residues: 236.3129 Evaluate side-chains 461 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 361 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 171 CYS Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 392 VAL Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 0.0270 chunk 27 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 203 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN D 323 GLN F 152 GLN F 172 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21048 Z= 0.151 Angle : 0.518 8.684 28586 Z= 0.267 Chirality : 0.039 0.189 3320 Planarity : 0.004 0.064 3509 Dihedral : 13.269 157.902 3125 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 4.96 % Allowed : 33.72 % Favored : 61.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.08 (0.18), residues: 2469 helix: 1.35 (0.16), residues: 1115 sheet: -0.09 (0.24), residues: 496 loop : -1.94 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 161 HIS 0.006 0.001 HIS C 267 PHE 0.012 0.001 PHE B 36 TYR 0.013 0.001 TYR C 274 ARG 0.006 0.000 ARG K 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 359 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.5167 (p90) REVERT: A 144 MET cc_start: 0.7516 (tmm) cc_final: 0.7262 (tpp) REVERT: B 57 LYS cc_start: 0.6307 (OUTLIER) cc_final: 0.5855 (tttm) REVERT: B 83 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6425 (ttp80) REVERT: C 113 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8422 (tt) REVERT: C 173 MET cc_start: 0.7240 (tpp) cc_final: 0.6972 (mtt) REVERT: C 250 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7372 (tmtp) REVERT: D 124 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.6167 (tttt) REVERT: D 149 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7735 (pt) REVERT: D 213 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7593 (t0) REVERT: E 202 LYS cc_start: 0.6993 (tmmt) cc_final: 0.6470 (ttmm) REVERT: E 233 CYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7031 (t) REVERT: F 267 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.5989 (mt) REVERT: F 349 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6943 (tmt) REVERT: G 24 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5879 (mp0) REVERT: G 98 ILE cc_start: 0.7753 (mt) cc_final: 0.7438 (mt) REVERT: G 145 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.4554 (p90) REVERT: K 230 ASN cc_start: 0.6624 (t160) cc_final: 0.6336 (t0) REVERT: K 268 GLN cc_start: 0.7157 (tm-30) cc_final: 0.6696 (tm-30) REVERT: K 322 LEU cc_start: 0.5687 (OUTLIER) cc_final: 0.5266 (mp) outliers start: 110 outliers final: 76 residues processed: 426 average time/residue: 0.3588 time to fit residues: 223.6718 Evaluate side-chains 447 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 357 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 171 CYS Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 119 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 189 optimal weight: 0.0170 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN F 152 GLN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21048 Z= 0.156 Angle : 0.522 10.272 28586 Z= 0.269 Chirality : 0.039 0.200 3320 Planarity : 0.004 0.064 3509 Dihedral : 13.211 157.064 3125 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.56 % Favored : 93.28 % Rotamer: Outliers : 4.87 % Allowed : 33.45 % Favored : 61.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.05 (0.18), residues: 2469 helix: 1.36 (0.16), residues: 1117 sheet: -0.06 (0.24), residues: 496 loop : -1.91 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 161 HIS 0.006 0.001 HIS C 267 PHE 0.023 0.001 PHE F 223 TYR 0.021 0.001 TYR C 274 ARG 0.004 0.000 ARG G 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 359 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.5273 (OUTLIER) cc_final: 0.5070 (p90) REVERT: A 144 MET cc_start: 0.7500 (tmm) cc_final: 0.7226 (tpp) REVERT: B 57 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5741 (tttm) REVERT: C 113 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8435 (tt) REVERT: C 172 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7451 (mmtt) REVERT: C 173 MET cc_start: 0.7258 (tpp) cc_final: 0.6969 (mtt) REVERT: C 250 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7404 (tmtp) REVERT: D 124 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.6163 (tttt) REVERT: D 149 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7744 (pt) REVERT: D 213 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7603 (t0) REVERT: E 202 LYS cc_start: 0.6988 (tmmt) cc_final: 0.6489 (ttmm) REVERT: E 233 CYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6998 (t) REVERT: F 267 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.5997 (mt) REVERT: F 349 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6890 (tmt) REVERT: G 24 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: G 98 ILE cc_start: 0.7793 (mt) cc_final: 0.7475 (mt) REVERT: G 145 PHE cc_start: 0.6030 (OUTLIER) cc_final: 0.4458 (p90) REVERT: K 230 ASN cc_start: 0.6595 (t160) cc_final: 0.6306 (t0) REVERT: K 268 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6684 (tm-30) REVERT: K 322 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5315 (mp) outliers start: 108 outliers final: 84 residues processed: 427 average time/residue: 0.3659 time to fit residues: 229.0454 Evaluate side-chains 452 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 355 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 171 CYS Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 392 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 210 optimal weight: 0.5980 chunk 224 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 202 optimal weight: 0.3980 chunk 212 optimal weight: 4.9990 chunk 223 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 HIS C 15 HIS F 152 GLN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21048 Z= 0.169 Angle : 0.534 13.011 28586 Z= 0.274 Chirality : 0.039 0.231 3320 Planarity : 0.004 0.064 3509 Dihedral : 13.171 157.159 3125 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.48 % Favored : 93.32 % Rotamer: Outliers : 5.23 % Allowed : 33.41 % Favored : 61.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.05 (0.18), residues: 2469 helix: 1.33 (0.16), residues: 1116 sheet: -0.03 (0.24), residues: 497 loop : -1.89 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 161 HIS 0.006 0.001 HIS C 267 PHE 0.029 0.001 PHE F 223 TYR 0.047 0.001 TYR C 274 ARG 0.005 0.000 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 358 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7488 (tmm) cc_final: 0.7220 (tpp) REVERT: B 57 LYS cc_start: 0.6209 (OUTLIER) cc_final: 0.5727 (tttm) REVERT: B 83 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6388 (ttp80) REVERT: C 113 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8438 (tt) REVERT: C 172 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7437 (mmtt) REVERT: C 173 MET cc_start: 0.7261 (tpp) cc_final: 0.6955 (mtt) REVERT: C 250 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7445 (tmtp) REVERT: D 124 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.6188 (tttt) REVERT: D 149 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7758 (pt) REVERT: D 213 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7572 (t0) REVERT: E 202 LYS cc_start: 0.7002 (tmmt) cc_final: 0.6503 (ttmm) REVERT: E 233 CYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7018 (t) REVERT: F 267 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6001 (mt) REVERT: F 349 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.6899 (tmt) REVERT: G 24 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5909 (mp0) REVERT: G 98 ILE cc_start: 0.7793 (mt) cc_final: 0.7484 (mt) REVERT: G 145 PHE cc_start: 0.6082 (OUTLIER) cc_final: 0.4489 (p90) REVERT: K 230 ASN cc_start: 0.6717 (t160) cc_final: 0.6409 (t0) REVERT: K 268 GLN cc_start: 0.7251 (tm-30) cc_final: 0.6991 (tm-30) REVERT: K 322 LEU cc_start: 0.5693 (OUTLIER) cc_final: 0.5254 (mp) REVERT: K 323 GLU cc_start: 0.5966 (mp0) cc_final: 0.5755 (mp0) outliers start: 116 outliers final: 94 residues processed: 434 average time/residue: 0.3610 time to fit residues: 230.2163 Evaluate side-chains 462 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 355 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 171 CYS Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 296 MET Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 392 VAL Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 444 MET Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 198 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 121 optimal weight: 0.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 HIS C 244 GLN F 172 ASN ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21048 Z= 0.200 Angle : 0.562 11.748 28586 Z= 0.287 Chirality : 0.040 0.237 3320 Planarity : 0.004 0.065 3509 Dihedral : 13.216 157.572 3125 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.97 % Favored : 92.83 % Rotamer: Outliers : 5.18 % Allowed : 33.36 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % 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: -0.10 (0.18), residues: 2469 helix: 1.26 (0.16), residues: 1117 sheet: -0.02 (0.24), residues: 502 loop : -1.90 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 55 HIS 0.005 0.001 HIS C 267 PHE 0.027 0.001 PHE C 240 TYR 0.034 0.001 TYR C 274 ARG 0.005 0.000 ARG K 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 352 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.5305 (OUTLIER) cc_final: 0.5017 (p90) REVERT: A 144 MET cc_start: 0.7463 (tmm) cc_final: 0.7219 (tpp) REVERT: B 57 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.5979 (tttm) REVERT: B 83 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6453 (ttp80) REVERT: C 113 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8466 (tt) REVERT: C 170 VAL cc_start: 0.6727 (OUTLIER) cc_final: 0.5515 (m) REVERT: C 172 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7488 (mmtt) REVERT: C 173 MET cc_start: 0.7289 (tpp) cc_final: 0.6964 (mtt) REVERT: C 250 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7559 (tmtp) REVERT: D 124 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6253 (tttt) REVERT: D 149 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7780 (pt) REVERT: E 202 LYS cc_start: 0.7040 (tmmt) cc_final: 0.6516 (ttmm) REVERT: E 233 CYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7051 (t) REVERT: F 267 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6038 (mt) REVERT: F 349 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.6904 (tmt) REVERT: G 24 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5948 (mp0) REVERT: G 145 PHE cc_start: 0.6100 (OUTLIER) cc_final: 0.4471 (p90) REVERT: K 230 ASN cc_start: 0.6739 (t160) cc_final: 0.6471 (t0) REVERT: K 268 GLN cc_start: 0.7328 (tm-30) cc_final: 0.7064 (tm-30) REVERT: K 322 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5320 (mp) REVERT: K 323 GLU cc_start: 0.6012 (mp0) cc_final: 0.5787 (mp0) REVERT: K 535 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7421 (mttm) REVERT: K 572 MET cc_start: 0.4071 (ptm) cc_final: 0.3657 (ptm) outliers start: 115 outliers final: 90 residues processed: 426 average time/residue: 0.3625 time to fit residues: 226.6319 Evaluate side-chains 454 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 350 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 15 HIS Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 193 CYS Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 171 CYS Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 269 HIS Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 333 SER Chi-restraints excluded: chain F residue 349 MET Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 91 ASN Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 145 PHE Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 203 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 296 SER Chi-restraints excluded: chain K residue 136 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain K residue 297 LYS Chi-restraints excluded: chain K residue 306 GLU Chi-restraints excluded: chain K residue 322 LEU Chi-restraints excluded: chain K residue 345 SER Chi-restraints excluded: chain K residue 400 LEU Chi-restraints excluded: chain K residue 425 GLU Chi-restraints excluded: chain K residue 432 LEU Chi-restraints excluded: chain K residue 441 MET Chi-restraints excluded: chain K residue 485 ASN Chi-restraints excluded: chain K residue 490 LEU Chi-restraints excluded: chain K residue 546 LEU Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain K residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 198 optimal weight: 0.0010 chunk 83 optimal weight: 0.0870 chunk 203 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 HIS ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.149359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133731 restraints weight = 28076.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136789 restraints weight = 16182.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138869 restraints weight = 10646.726| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21048 Z= 0.158 Angle : 0.538 11.539 28586 Z= 0.276 Chirality : 0.039 0.215 3320 Planarity : 0.004 0.068 3509 Dihedral : 13.161 158.732 3125 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.28 % Favored : 93.52 % Rotamer: Outliers : 4.64 % Allowed : 34.40 % Favored : 60.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2469 helix: 1.31 (0.16), residues: 1116 sheet: 0.02 (0.24), residues: 503 loop : -1.84 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 161 HIS 0.005 0.001 HIS C 267 PHE 0.016 0.001 PHE C 263 TYR 0.037 0.001 TYR C 274 ARG 0.007 0.000 ARG G 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4723.33 seconds wall clock time: 86 minutes 22.99 seconds (5182.99 seconds total)