Starting phenix.real_space_refine on Wed Feb 14 19:57:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bty_30191/02_2024/7bty_30191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bty_30191/02_2024/7bty_30191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bty_30191/02_2024/7bty_30191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bty_30191/02_2024/7bty_30191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bty_30191/02_2024/7bty_30191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bty_30191/02_2024/7bty_30191.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6512 2.51 5 N 1724 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 148": "OD1" <-> "OD2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 152": "OD1" <-> "OD2" Residue "L ARG 160": "NH1" <-> "NH2" Residue "L PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 192": "NH1" <-> "NH2" Residue "L ASP 203": "OD1" <-> "OD2" Residue "L ARG 209": "NH1" <-> "NH2" Residue "L ARG 263": "NH1" <-> "NH2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L ASP 424": "OD1" <-> "OD2" Residue "L GLU 432": "OE1" <-> "OE2" Residue "L PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2399 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 2 Chain: "C" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2439 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2555 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.63, per 1000 atoms: 0.55 Number of scatterers: 10168 At special positions: 0 Unit cell: (100.845, 104.58, 108.315, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1888 8.00 N 1724 7.00 C 6512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 32.3% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.586A pdb=" N LYS A 201 " --> pdb=" O TRP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.512A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.978A pdb=" N ILE A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.510A pdb=" N GLN B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.546A pdb=" N ASN B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 169 through 181 Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.817A pdb=" N MET B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.621A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.621A pdb=" N SER B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.702A pdb=" N GLN B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.631A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.540A pdb=" N GLN B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.559A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.711A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.780A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 122 through 132 removed outlier: 3.597A pdb=" N PHE C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.591A pdb=" N ASN C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 203 through 206 removed outlier: 3.649A pdb=" N HIS C 206 " --> pdb=" O LYS C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 203 through 206' Processing helix chain 'C' and resid 207 through 227 removed outlier: 3.788A pdb=" N LYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.583A pdb=" N SER C 234 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 removed outlier: 3.766A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.018A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.927A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 324 removed outlier: 3.576A pdb=" N TYR C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 17 removed outlier: 4.122A pdb=" N ARG L 10 " --> pdb=" O ASP L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 81 through 87 removed outlier: 4.033A pdb=" N ARG L 86 " --> pdb=" O LYS L 83 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN L 87 " --> pdb=" O PHE L 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.603A pdb=" N TYR A 140 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA A 139 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 164 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 175 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A 170 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 194 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 464 through 466 removed outlier: 7.305A pdb=" N ALA A 465 " --> pdb=" O TYR B 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.459A pdb=" N THR C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 47 removed outlier: 6.683A pdb=" N ILE C 46 " --> pdb=" O ARG C 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 44 through 52 removed outlier: 3.624A pdb=" N ASN L 57 " --> pdb=" O ASN L 49 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP L 60 " --> pdb=" O ASN L 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 179 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 195 " --> pdb=" O ARG L 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 209 through 210 removed outlier: 4.085A pdb=" N VAL L 210 " --> pdb=" O ALA L 235 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR L 251 " --> pdb=" O GLY L 234 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU L 236 " --> pdb=" O SER L 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 249 " --> pdb=" O GLU L 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 230 through 231 removed outlier: 3.715A pdb=" N TYR L 255 " --> pdb=" O SER L 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 282 through 284 Processing sheet with id=AB2, first strand: chain 'L' and resid 413 through 421 removed outlier: 3.764A pdb=" N THR L 413 " --> pdb=" O LYS L 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER L 421 " --> pdb=" O THR L 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 426 " --> pdb=" O SER L 421 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU L 445 " --> pdb=" O LYS L 484 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS L 484 " --> pdb=" O GLU L 445 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL L 447 " --> pdb=" O PRO L 482 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 413 through 421 removed outlier: 3.764A pdb=" N THR L 413 " --> pdb=" O LYS L 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER L 421 " --> pdb=" O THR L 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 426 " --> pdb=" O SER L 421 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2 1.15 - 1.32: 1686 1.32 - 1.49: 4442 1.49 - 1.66: 4191 1.66 - 1.83: 65 Bond restraints: 10386 Sorted by residual: bond pdb=" C GLN A 433 " pdb=" O GLN A 433 " ideal model delta sigma weight residual 1.233 0.979 0.254 1.46e-02 4.69e+03 3.03e+02 bond pdb=" CA GLN A 433 " pdb=" C GLN A 433 " ideal model delta sigma weight residual 1.520 1.322 0.197 1.40e-02 5.10e+03 1.99e+02 bond pdb=" CA GLN A 433 " pdb=" CB GLN A 433 " ideal model delta sigma weight residual 1.537 1.402 0.134 1.67e-02 3.59e+03 6.46e+01 bond pdb=" C GLN A 433 " pdb=" N LEU A 434 " ideal model delta sigma weight residual 1.333 1.232 0.101 1.49e-02 4.50e+03 4.57e+01 bond pdb=" CD GLN A 433 " pdb=" NE2 GLN A 433 " ideal model delta sigma weight residual 1.328 1.186 0.142 2.10e-02 2.27e+03 4.56e+01 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.49: 150 105.49 - 113.00: 5526 113.00 - 120.51: 4422 120.51 - 128.01: 3835 128.01 - 135.52: 101 Bond angle restraints: 14034 Sorted by residual: angle pdb=" C ALA B 127 " pdb=" N LEU B 128 " pdb=" CA LEU B 128 " ideal model delta sigma weight residual 122.37 113.15 9.22 9.30e-01 1.16e+00 9.84e+01 angle pdb=" N GLU C 98 " pdb=" CA GLU C 98 " pdb=" C GLU C 98 " ideal model delta sigma weight residual 110.80 128.50 -17.70 2.13e+00 2.20e-01 6.90e+01 angle pdb=" C THR C 87 " pdb=" N SER C 88 " pdb=" CA SER C 88 " ideal model delta sigma weight residual 121.70 135.52 -13.82 1.80e+00 3.09e-01 5.90e+01 angle pdb=" C TYR L 147 " pdb=" N TYR L 148 " pdb=" CA TYR L 148 " ideal model delta sigma weight residual 123.21 114.20 9.01 1.19e+00 7.06e-01 5.74e+01 angle pdb=" CA THR C 87 " pdb=" C THR C 87 " pdb=" N SER C 88 " ideal model delta sigma weight residual 116.84 104.59 12.25 1.71e+00 3.42e-01 5.13e+01 ... (remaining 14029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5332 17.20 - 34.39: 682 34.39 - 51.59: 147 51.59 - 68.79: 13 68.79 - 85.98: 12 Dihedral angle restraints: 6186 sinusoidal: 2480 harmonic: 3706 Sorted by residual: dihedral pdb=" CA LEU B 128 " pdb=" C LEU B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 115.98 64.02 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" N GLU C 98 " pdb=" C GLU C 98 " pdb=" CA GLU C 98 " pdb=" CB GLU C 98 " ideal model delta harmonic sigma weight residual 122.80 150.43 -27.63 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" C GLU C 98 " pdb=" N GLU C 98 " pdb=" CA GLU C 98 " pdb=" CB GLU C 98 " ideal model delta harmonic sigma weight residual -122.60 -149.54 26.94 0 2.50e+00 1.60e-01 1.16e+02 ... (remaining 6183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 1570 0.265 - 0.529: 2 0.529 - 0.794: 0 0.794 - 1.058: 0 1.058 - 1.323: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CA GLU C 98 " pdb=" N GLU C 98 " pdb=" C GLU C 98 " pdb=" CB GLU C 98 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.32 2.00e-01 2.50e+01 4.37e+01 chirality pdb=" CA GLN A 433 " pdb=" N GLN A 433 " pdb=" C GLN A 433 " pdb=" CB GLN A 433 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA GLU C 97 " pdb=" N GLU C 97 " pdb=" C GLU C 97 " pdb=" CB GLU C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1570 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 87 " 0.046 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C THR C 87 " -0.173 2.00e-02 2.50e+03 pdb=" O THR C 87 " 0.071 2.00e-02 2.50e+03 pdb=" N SER C 88 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " 0.093 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO C 61 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 432 " 0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C GLY A 432 " -0.083 2.00e-02 2.50e+03 pdb=" O GLY A 432 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN A 433 " 0.029 2.00e-02 2.50e+03 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2304 2.78 - 3.31: 8310 3.31 - 3.84: 16242 3.84 - 4.37: 20023 4.37 - 4.90: 35344 Nonbonded interactions: 82223 Sorted by model distance: nonbonded pdb=" O GLN C 230 " pdb=" OG SER C 234 " model vdw 2.247 2.440 nonbonded pdb=" OG SER B 184 " pdb=" OE2 GLU B 301 " model vdw 2.254 2.440 nonbonded pdb=" O THR B 165 " pdb=" OG1 THR B 169 " model vdw 2.266 2.440 nonbonded pdb=" OG1 THR A 265 " pdb=" OD2 ASP A 377 " model vdw 2.279 2.440 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.279 2.440 ... (remaining 82218 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.830 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.260 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.010 0.254 10386 Z= 0.658 Angle : 1.151 17.699 14034 Z= 0.638 Chirality : 0.069 1.323 1573 Planarity : 0.009 0.139 1764 Dihedral : 15.857 85.983 3786 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.23 % Favored : 89.13 % Rotamer: Outliers : 0.70 % Allowed : 11.89 % Favored : 87.40 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.66 % 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: -5.57 (0.18), residues: 1242 helix: -4.33 (0.13), residues: 362 sheet: -3.05 (0.22), residues: 396 loop : -3.44 (0.22), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 323 HIS 0.012 0.002 HIS A 310 PHE 0.038 0.003 PHE B 68 TYR 0.029 0.003 TYR A 140 ARG 0.010 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.207 Fit side-chains REVERT: A 300 LYS cc_start: 0.8372 (tttt) cc_final: 0.8104 (tttm) REVERT: A 385 ASP cc_start: 0.8050 (m-30) cc_final: 0.7394 (m-30) REVERT: B 136 LYS cc_start: 0.8181 (mttp) cc_final: 0.7906 (mmtt) REVERT: B 189 MET cc_start: 0.9165 (mmm) cc_final: 0.8276 (mmt) REVERT: B 236 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7442 (pm20) REVERT: C 11 LYS cc_start: 0.7420 (ptmt) cc_final: 0.7157 (ptmt) REVERT: C 40 MET cc_start: 0.9016 (ptt) cc_final: 0.8773 (ptm) REVERT: C 102 ILE cc_start: 0.8568 (mm) cc_final: 0.8175 (mm) REVERT: C 111 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7903 (tp30) REVERT: C 121 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7115 (mm-30) REVERT: C 150 TYR cc_start: 0.8141 (m-80) cc_final: 0.7840 (m-80) REVERT: C 317 MET cc_start: 0.8282 (tpp) cc_final: 0.7934 (tpp) REVERT: L 5 MET cc_start: 0.6691 (ttp) cc_final: 0.6314 (ttp) REVERT: L 146 MET cc_start: 0.8010 (ptp) cc_final: 0.7545 (ptm) REVERT: L 168 MET cc_start: 0.7353 (mtp) cc_final: 0.7125 (mtp) REVERT: L 254 TYR cc_start: 0.7447 (t80) cc_final: 0.6703 (t80) outliers start: 8 outliers final: 3 residues processed: 163 average time/residue: 0.2647 time to fit residues: 57.9608 Evaluate side-chains 122 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 98 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 GLN A 269 GLN A 273 GLN A 280 HIS A 303 ASN A 369 GLN A 411 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 87 GLN B 94 ASN B 101 HIS ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 HIS C 129 GLN C 133 ASN C 224 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN C 262 GLN C 285 ASN L 57 ASN L 195 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10386 Z= 0.276 Angle : 0.708 8.993 14034 Z= 0.373 Chirality : 0.044 0.222 1573 Planarity : 0.007 0.107 1764 Dihedral : 7.726 67.513 1366 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.02 % Favored : 90.74 % Rotamer: Outliers : 2.03 % Allowed : 15.33 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.33 % 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: -4.09 (0.21), residues: 1242 helix: -2.25 (0.22), residues: 363 sheet: -2.50 (0.24), residues: 398 loop : -3.05 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 310 PHE 0.021 0.002 PHE B 18 TYR 0.020 0.002 TYR B 164 ARG 0.003 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.191 Fit side-chains REVERT: A 161 GLU cc_start: 0.7819 (tt0) cc_final: 0.7012 (mt-10) REVERT: A 266 MET cc_start: 0.8916 (mmt) cc_final: 0.8607 (mmm) REVERT: A 300 LYS cc_start: 0.8335 (tttt) cc_final: 0.8058 (tttm) REVERT: A 385 ASP cc_start: 0.8058 (m-30) cc_final: 0.7448 (m-30) REVERT: A 390 TYR cc_start: 0.8730 (p90) cc_final: 0.8348 (p90) REVERT: B 136 LYS cc_start: 0.8035 (mttp) cc_final: 0.7728 (mmtt) REVERT: B 189 MET cc_start: 0.9062 (mmm) cc_final: 0.8195 (mmt) REVERT: B 190 GLU cc_start: 0.7929 (tt0) cc_final: 0.7711 (tt0) REVERT: C 11 LYS cc_start: 0.7341 (ptmt) cc_final: 0.7104 (ptmt) REVERT: C 66 ASP cc_start: 0.4632 (p0) cc_final: 0.4342 (p0) REVERT: C 102 ILE cc_start: 0.8214 (mm) cc_final: 0.7926 (mm) REVERT: C 260 TYR cc_start: 0.7797 (t80) cc_final: 0.7433 (t80) REVERT: C 317 MET cc_start: 0.8191 (tpp) cc_final: 0.7876 (tpp) REVERT: L 60 ASP cc_start: 0.8056 (p0) cc_final: 0.7854 (p0) REVERT: L 146 MET cc_start: 0.8017 (ptp) cc_final: 0.7784 (ptm) REVERT: L 168 MET cc_start: 0.7362 (mtp) cc_final: 0.7130 (mtp) outliers start: 23 outliers final: 16 residues processed: 154 average time/residue: 0.2396 time to fit residues: 51.6893 Evaluate side-chains 134 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain L residue 139 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 178 GLN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 133 ASN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10386 Z= 0.413 Angle : 0.751 7.457 14034 Z= 0.390 Chirality : 0.047 0.175 1573 Planarity : 0.007 0.119 1764 Dihedral : 7.356 64.002 1363 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.39 % Favored : 89.29 % Rotamer: Outliers : 3.44 % Allowed : 17.00 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.22), residues: 1242 helix: -1.14 (0.26), residues: 358 sheet: -2.30 (0.25), residues: 390 loop : -2.97 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 323 HIS 0.007 0.001 HIS A 310 PHE 0.026 0.002 PHE B 18 TYR 0.023 0.002 TYR A 140 ARG 0.006 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 1.129 Fit side-chains REVERT: A 266 MET cc_start: 0.8906 (mmt) cc_final: 0.8610 (mmm) REVERT: A 300 LYS cc_start: 0.8333 (tttt) cc_final: 0.8034 (tttm) REVERT: A 385 ASP cc_start: 0.8083 (m-30) cc_final: 0.7486 (m-30) REVERT: A 390 TYR cc_start: 0.8783 (p90) cc_final: 0.8390 (p90) REVERT: A 446 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8763 (tt) REVERT: B 136 LYS cc_start: 0.8001 (mttp) cc_final: 0.7715 (mmtt) REVERT: B 189 MET cc_start: 0.9067 (mmm) cc_final: 0.8215 (mmt) REVERT: B 190 GLU cc_start: 0.8047 (tt0) cc_final: 0.7834 (tt0) REVERT: C 11 LYS cc_start: 0.7313 (ptmt) cc_final: 0.7002 (ptmt) REVERT: C 66 ASP cc_start: 0.4838 (p0) cc_final: 0.4630 (p0) REVERT: C 102 ILE cc_start: 0.8298 (mm) cc_final: 0.8022 (mm) REVERT: C 111 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: C 119 ASP cc_start: 0.7515 (t0) cc_final: 0.7153 (t0) REVERT: C 317 MET cc_start: 0.8195 (tpp) cc_final: 0.7917 (tpp) REVERT: L 13 TYR cc_start: 0.6575 (m-10) cc_final: 0.5997 (m-80) REVERT: L 146 MET cc_start: 0.8094 (ptp) cc_final: 0.7829 (ptm) REVERT: L 254 TYR cc_start: 0.7208 (t80) cc_final: 0.6757 (t80) outliers start: 39 outliers final: 25 residues processed: 152 average time/residue: 0.2213 time to fit residues: 47.2461 Evaluate side-chains 143 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN B 318 GLN B 326 ASN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10386 Z= 0.156 Angle : 0.585 8.139 14034 Z= 0.306 Chirality : 0.041 0.159 1573 Planarity : 0.005 0.095 1764 Dihedral : 6.578 68.866 1363 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.45 % Favored : 91.30 % Rotamer: Outliers : 2.11 % Allowed : 18.94 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.23), residues: 1242 helix: -0.32 (0.27), residues: 372 sheet: -1.86 (0.26), residues: 386 loop : -2.97 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 323 HIS 0.003 0.000 HIS A 310 PHE 0.016 0.001 PHE B 18 TYR 0.015 0.001 TYR C 260 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.166 Fit side-chains REVERT: A 157 ARG cc_start: 0.7540 (ptt90) cc_final: 0.7313 (ptt180) REVERT: A 161 GLU cc_start: 0.7677 (tt0) cc_final: 0.6929 (mt-10) REVERT: A 266 MET cc_start: 0.8924 (mmt) cc_final: 0.8616 (mmm) REVERT: A 277 ILE cc_start: 0.8907 (tt) cc_final: 0.8488 (pt) REVERT: A 300 LYS cc_start: 0.8369 (tttt) cc_final: 0.8084 (tttm) REVERT: A 385 ASP cc_start: 0.8046 (m-30) cc_final: 0.7405 (m-30) REVERT: A 390 TYR cc_start: 0.8575 (p90) cc_final: 0.8217 (p90) REVERT: A 446 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 136 LYS cc_start: 0.7937 (mttp) cc_final: 0.7658 (mmtt) REVERT: B 178 GLN cc_start: 0.8477 (mt0) cc_final: 0.8153 (tt0) REVERT: B 189 MET cc_start: 0.9015 (mmm) cc_final: 0.8116 (mmt) REVERT: C 11 LYS cc_start: 0.7263 (ptmt) cc_final: 0.6951 (ptmt) REVERT: C 40 MET cc_start: 0.8905 (ptt) cc_final: 0.8680 (ptm) REVERT: C 102 ILE cc_start: 0.8013 (mm) cc_final: 0.7797 (mm) REVERT: C 260 TYR cc_start: 0.7584 (t80) cc_final: 0.7213 (t80) REVERT: C 303 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7111 (pt0) REVERT: C 317 MET cc_start: 0.8253 (tpp) cc_final: 0.7975 (tpp) REVERT: L 13 TYR cc_start: 0.6523 (m-10) cc_final: 0.5610 (m-80) REVERT: L 85 MET cc_start: 0.2096 (mmp) cc_final: 0.1276 (mtp) REVERT: L 166 GLN cc_start: 0.8361 (mt0) cc_final: 0.7760 (tt0) REVERT: L 254 TYR cc_start: 0.7279 (t80) cc_final: 0.6768 (t80) outliers start: 24 outliers final: 13 residues processed: 158 average time/residue: 0.2328 time to fit residues: 50.9900 Evaluate side-chains 137 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 285 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0980 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 82 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN C 50 ASN L 49 ASN L 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10386 Z= 0.133 Angle : 0.563 9.272 14034 Z= 0.292 Chirality : 0.040 0.237 1573 Planarity : 0.005 0.091 1764 Dihedral : 6.204 68.838 1361 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.45 % Favored : 91.30 % Rotamer: Outliers : 2.20 % Allowed : 20.26 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.24), residues: 1242 helix: 0.24 (0.28), residues: 367 sheet: -1.62 (0.26), residues: 391 loop : -2.77 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 323 HIS 0.002 0.000 HIS A 310 PHE 0.023 0.001 PHE L 485 TYR 0.013 0.001 TYR C 260 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.118 Fit side-chains REVERT: A 266 MET cc_start: 0.8938 (mmt) cc_final: 0.8609 (mmm) REVERT: A 277 ILE cc_start: 0.8712 (tt) cc_final: 0.8393 (pt) REVERT: A 300 LYS cc_start: 0.8358 (tttt) cc_final: 0.8084 (tttm) REVERT: A 385 ASP cc_start: 0.7929 (m-30) cc_final: 0.7501 (m-30) REVERT: A 390 TYR cc_start: 0.8471 (p90) cc_final: 0.8107 (p90) REVERT: A 455 PHE cc_start: 0.8140 (m-80) cc_final: 0.7928 (m-80) REVERT: B 150 MET cc_start: 0.8958 (mmm) cc_final: 0.8638 (mmp) REVERT: B 178 GLN cc_start: 0.8510 (mt0) cc_final: 0.8192 (tt0) REVERT: B 189 MET cc_start: 0.9042 (mmm) cc_final: 0.8095 (mmt) REVERT: B 308 PHE cc_start: 0.8700 (t80) cc_final: 0.8330 (t80) REVERT: C 11 LYS cc_start: 0.7414 (ptmt) cc_final: 0.7069 (ptmt) REVERT: C 40 MET cc_start: 0.8914 (ptt) cc_final: 0.8631 (ptm) REVERT: C 102 ILE cc_start: 0.8010 (mm) cc_final: 0.7795 (mm) REVERT: C 260 TYR cc_start: 0.7447 (t80) cc_final: 0.7067 (t80) REVERT: C 303 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7189 (pt0) REVERT: C 317 MET cc_start: 0.8286 (tpp) cc_final: 0.7964 (tpp) REVERT: L 13 TYR cc_start: 0.6509 (m-10) cc_final: 0.5664 (m-80) REVERT: L 85 MET cc_start: 0.1546 (mmp) cc_final: 0.0280 (ttm) REVERT: L 166 GLN cc_start: 0.8256 (mt0) cc_final: 0.7926 (tt0) REVERT: L 169 LEU cc_start: 0.8473 (mt) cc_final: 0.8008 (tt) REVERT: L 253 ARG cc_start: 0.7514 (ptt-90) cc_final: 0.7264 (ptt-90) REVERT: L 254 TYR cc_start: 0.7309 (t80) cc_final: 0.6823 (t80) outliers start: 25 outliers final: 16 residues processed: 158 average time/residue: 0.2397 time to fit residues: 52.2499 Evaluate side-chains 138 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10386 Z= 0.304 Angle : 0.669 8.841 14034 Z= 0.343 Chirality : 0.044 0.191 1573 Planarity : 0.005 0.105 1764 Dihedral : 6.582 69.176 1361 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.66 % Favored : 90.02 % Rotamer: Outliers : 3.52 % Allowed : 20.62 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.24), residues: 1242 helix: 0.09 (0.28), residues: 373 sheet: -1.68 (0.26), residues: 397 loop : -2.89 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 236 HIS 0.004 0.001 HIS A 422 PHE 0.023 0.002 PHE L 298 TYR 0.022 0.002 TYR B 164 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.203 Fit side-chains REVERT: A 266 MET cc_start: 0.8922 (mmt) cc_final: 0.8629 (mmm) REVERT: A 299 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8733 (tt) REVERT: A 300 LYS cc_start: 0.8409 (tttt) cc_final: 0.8149 (tttm) REVERT: A 385 ASP cc_start: 0.7937 (m-30) cc_final: 0.7341 (m-30) REVERT: A 390 TYR cc_start: 0.8724 (p90) cc_final: 0.8352 (p90) REVERT: B 189 MET cc_start: 0.9080 (mmm) cc_final: 0.8265 (mmt) REVERT: C 11 LYS cc_start: 0.7486 (ptmt) cc_final: 0.7164 (ptmt) REVERT: C 40 MET cc_start: 0.8953 (ptt) cc_final: 0.8706 (ptm) REVERT: C 102 ILE cc_start: 0.8092 (mm) cc_final: 0.7851 (mm) REVERT: C 111 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: C 119 ASP cc_start: 0.7477 (t0) cc_final: 0.7162 (t0) REVERT: C 303 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: L 13 TYR cc_start: 0.6567 (m-10) cc_final: 0.5915 (m-80) REVERT: L 85 MET cc_start: 0.1362 (mmp) cc_final: 0.0186 (ttm) REVERT: L 169 LEU cc_start: 0.8320 (mt) cc_final: 0.8068 (tt) REVERT: L 253 ARG cc_start: 0.7494 (ptt-90) cc_final: 0.7260 (ptt90) REVERT: L 254 TYR cc_start: 0.7409 (t80) cc_final: 0.6823 (t80) outliers start: 40 outliers final: 29 residues processed: 149 average time/residue: 0.2224 time to fit residues: 46.7014 Evaluate side-chains 149 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 285 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10386 Z= 0.358 Angle : 0.694 7.433 14034 Z= 0.357 Chirality : 0.046 0.226 1573 Planarity : 0.005 0.105 1764 Dihedral : 6.770 69.508 1361 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.90 % Favored : 89.86 % Rotamer: Outliers : 3.88 % Allowed : 20.18 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.24), residues: 1242 helix: 0.08 (0.28), residues: 365 sheet: -1.74 (0.26), residues: 390 loop : -2.88 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 301 HIS 0.004 0.001 HIS A 169 PHE 0.024 0.002 PHE L 485 TYR 0.021 0.002 TYR B 164 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 118 time to evaluate : 1.157 Fit side-chains REVERT: A 266 MET cc_start: 0.8915 (mmt) cc_final: 0.8608 (mmm) REVERT: A 300 LYS cc_start: 0.8357 (tttt) cc_final: 0.8088 (tttm) REVERT: A 385 ASP cc_start: 0.8021 (m-30) cc_final: 0.7430 (m-30) REVERT: A 390 TYR cc_start: 0.8741 (p90) cc_final: 0.8334 (p90) REVERT: B 189 MET cc_start: 0.9085 (mmm) cc_final: 0.8261 (mmt) REVERT: C 11 LYS cc_start: 0.7405 (ptmt) cc_final: 0.7064 (ptmt) REVERT: C 40 MET cc_start: 0.8957 (ptt) cc_final: 0.8736 (ptm) REVERT: C 102 ILE cc_start: 0.8180 (mm) cc_final: 0.7937 (mm) REVERT: C 111 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: C 119 ASP cc_start: 0.7493 (t0) cc_final: 0.7170 (t0) REVERT: C 303 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7143 (pt0) REVERT: L 13 TYR cc_start: 0.6504 (m-10) cc_final: 0.5956 (m-80) REVERT: L 85 MET cc_start: 0.1508 (mmp) cc_final: 0.0242 (ttm) REVERT: L 166 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: L 254 TYR cc_start: 0.7465 (t80) cc_final: 0.6880 (t80) outliers start: 44 outliers final: 33 residues processed: 147 average time/residue: 0.2213 time to fit residues: 46.0823 Evaluate side-chains 154 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 285 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10386 Z= 0.165 Angle : 0.592 7.483 14034 Z= 0.306 Chirality : 0.042 0.215 1573 Planarity : 0.005 0.095 1764 Dihedral : 6.321 71.597 1361 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.70 % Favored : 91.06 % Rotamer: Outliers : 3.17 % Allowed : 20.62 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.24), residues: 1242 helix: 0.44 (0.28), residues: 368 sheet: -1.57 (0.26), residues: 397 loop : -2.81 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.003 0.000 HIS A 310 PHE 0.026 0.001 PHE L 485 TYR 0.013 0.001 TYR B 164 ARG 0.002 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.269 Fit side-chains REVERT: A 266 MET cc_start: 0.8947 (mmt) cc_final: 0.8616 (mmm) REVERT: A 300 LYS cc_start: 0.8347 (tttt) cc_final: 0.8068 (tttm) REVERT: A 385 ASP cc_start: 0.7930 (m-30) cc_final: 0.7319 (m-30) REVERT: A 390 TYR cc_start: 0.8522 (p90) cc_final: 0.8207 (p90) REVERT: A 455 PHE cc_start: 0.8193 (m-80) cc_final: 0.7984 (m-80) REVERT: B 189 MET cc_start: 0.9035 (mmm) cc_final: 0.8229 (mmt) REVERT: C 11 LYS cc_start: 0.7320 (ptmt) cc_final: 0.6964 (ptmt) REVERT: C 102 ILE cc_start: 0.8141 (mm) cc_final: 0.7939 (mm) REVERT: C 111 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: C 119 ASP cc_start: 0.7375 (t0) cc_final: 0.7047 (t0) REVERT: C 260 TYR cc_start: 0.7653 (t80) cc_final: 0.7298 (t80) REVERT: C 303 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7126 (pt0) REVERT: L 13 TYR cc_start: 0.6423 (m-10) cc_final: 0.5607 (m-80) REVERT: L 85 MET cc_start: 0.1776 (mmp) cc_final: 0.0488 (ttm) REVERT: L 166 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: L 169 LEU cc_start: 0.8267 (mt) cc_final: 0.8052 (tt) REVERT: L 231 LEU cc_start: 0.8382 (tt) cc_final: 0.7816 (pp) REVERT: L 254 TYR cc_start: 0.7415 (t80) cc_final: 0.6787 (t80) REVERT: L 435 TRP cc_start: 0.6976 (OUTLIER) cc_final: 0.5605 (t60) outliers start: 36 outliers final: 26 residues processed: 143 average time/residue: 0.2335 time to fit residues: 46.7128 Evaluate side-chains 147 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 285 LYS Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10386 Z= 0.307 Angle : 0.684 15.419 14034 Z= 0.346 Chirality : 0.044 0.199 1573 Planarity : 0.005 0.104 1764 Dihedral : 6.579 71.561 1361 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.06 % Favored : 89.61 % Rotamer: Outliers : 3.17 % Allowed : 20.53 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.24), residues: 1242 helix: 0.32 (0.28), residues: 372 sheet: -1.63 (0.26), residues: 400 loop : -2.89 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.003 0.001 HIS A 411 PHE 0.023 0.002 PHE L 485 TYR 0.020 0.002 TYR B 164 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 1.754 Fit side-chains REVERT: A 161 GLU cc_start: 0.7690 (tt0) cc_final: 0.7009 (mt-10) REVERT: A 266 MET cc_start: 0.8921 (mmt) cc_final: 0.8626 (mmm) REVERT: A 300 LYS cc_start: 0.8408 (tttt) cc_final: 0.8120 (tttm) REVERT: A 335 ILE cc_start: 0.8495 (mp) cc_final: 0.8293 (mt) REVERT: A 385 ASP cc_start: 0.7922 (m-30) cc_final: 0.7326 (m-30) REVERT: A 390 TYR cc_start: 0.8690 (p90) cc_final: 0.8308 (p90) REVERT: B 189 MET cc_start: 0.9076 (mmm) cc_final: 0.8250 (mmt) REVERT: C 11 LYS cc_start: 0.7368 (ptmt) cc_final: 0.7024 (ptmt) REVERT: C 40 MET cc_start: 0.8959 (ptt) cc_final: 0.8693 (ptm) REVERT: C 102 ILE cc_start: 0.8077 (mm) cc_final: 0.7837 (mm) REVERT: C 111 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: C 119 ASP cc_start: 0.7431 (t0) cc_final: 0.7096 (t0) REVERT: C 303 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7198 (pt0) REVERT: L 13 TYR cc_start: 0.6458 (m-10) cc_final: 0.5950 (m-80) REVERT: L 85 MET cc_start: 0.1642 (mmp) cc_final: 0.0258 (ttm) REVERT: L 166 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: L 169 LEU cc_start: 0.8279 (mt) cc_final: 0.8073 (tt) REVERT: L 231 LEU cc_start: 0.8223 (tt) cc_final: 0.7660 (pp) REVERT: L 254 TYR cc_start: 0.7577 (t80) cc_final: 0.6650 (t80) REVERT: L 435 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.6674 (t60) outliers start: 36 outliers final: 29 residues processed: 141 average time/residue: 0.2325 time to fit residues: 46.2063 Evaluate side-chains 147 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 285 LYS Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 9.9990 chunk 71 optimal weight: 0.0050 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10386 Z= 0.223 Angle : 0.645 14.424 14034 Z= 0.325 Chirality : 0.043 0.197 1573 Planarity : 0.005 0.099 1764 Dihedral : 6.413 73.069 1361 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.78 % Favored : 90.98 % Rotamer: Outliers : 3.17 % Allowed : 20.70 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.24), residues: 1242 helix: 0.48 (0.28), residues: 374 sheet: -1.54 (0.27), residues: 397 loop : -2.87 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 301 HIS 0.003 0.001 HIS A 310 PHE 0.026 0.002 PHE L 485 TYR 0.016 0.002 TYR B 164 ARG 0.007 0.000 ARG L 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 1.087 Fit side-chains REVERT: A 266 MET cc_start: 0.8941 (mmt) cc_final: 0.8619 (mmm) REVERT: A 300 LYS cc_start: 0.8365 (tttt) cc_final: 0.8100 (tttm) REVERT: A 385 ASP cc_start: 0.7958 (m-30) cc_final: 0.7342 (m-30) REVERT: A 390 TYR cc_start: 0.8612 (p90) cc_final: 0.8272 (p90) REVERT: A 455 PHE cc_start: 0.8235 (m-80) cc_final: 0.8031 (m-80) REVERT: B 189 MET cc_start: 0.9052 (mmm) cc_final: 0.8211 (mmt) REVERT: C 11 LYS cc_start: 0.7344 (ptmt) cc_final: 0.7006 (ptmt) REVERT: C 40 MET cc_start: 0.8943 (ptt) cc_final: 0.8697 (ptm) REVERT: C 102 ILE cc_start: 0.8083 (mm) cc_final: 0.7871 (mm) REVERT: C 111 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: C 119 ASP cc_start: 0.7398 (t0) cc_final: 0.7062 (t0) REVERT: C 260 TYR cc_start: 0.7826 (t80) cc_final: 0.7479 (t80) REVERT: C 303 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: L 13 TYR cc_start: 0.6431 (m-10) cc_final: 0.5919 (m-80) REVERT: L 85 MET cc_start: 0.1965 (mmp) cc_final: 0.0549 (ttm) REVERT: L 166 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: L 169 LEU cc_start: 0.8452 (mt) cc_final: 0.8068 (tt) REVERT: L 231 LEU cc_start: 0.8139 (tt) cc_final: 0.7593 (pp) REVERT: L 254 TYR cc_start: 0.7508 (t80) cc_final: 0.6424 (t80) REVERT: L 435 TRP cc_start: 0.6917 (OUTLIER) cc_final: 0.6700 (t60) outliers start: 36 outliers final: 31 residues processed: 145 average time/residue: 0.2248 time to fit residues: 45.8456 Evaluate side-chains 155 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 187 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 285 LYS Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.172827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.123693 restraints weight = 10612.105| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.83 r_work: 0.3106 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10386 Z= 0.273 Angle : 0.906 59.192 14034 Z= 0.510 Chirality : 0.051 1.057 1573 Planarity : 0.006 0.102 1764 Dihedral : 6.490 73.035 1361 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer: Outliers : 3.35 % Allowed : 20.62 % Favored : 76.04 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.24), residues: 1242 helix: 0.48 (0.28), residues: 374 sheet: -1.56 (0.27), residues: 397 loop : -2.87 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.003 0.001 HIS A 310 PHE 0.024 0.002 PHE L 485 TYR 0.017 0.002 TYR B 164 ARG 0.006 0.000 ARG L 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2149.68 seconds wall clock time: 40 minutes 10.28 seconds (2410.28 seconds total)