Starting phenix.real_space_refine on Fri Dec 8 23:40:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lml_0918/12_2023/6lml_0918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lml_0918/12_2023/6lml_0918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lml_0918/12_2023/6lml_0918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lml_0918/12_2023/6lml_0918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lml_0918/12_2023/6lml_0918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lml_0918/12_2023/6lml_0918.pdb" } resolution = 3.9 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= 0.002 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 59 5.16 5 C 6036 2.51 5 N 1625 2.21 5 O 1718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 124": "OD1" <-> "OD2" Residue "R GLU 127": "OE1" <-> "OE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 417": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9438 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1735 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2322 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 300} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 241 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 245 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3153 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 5.51, per 1000 atoms: 0.58 Number of scatterers: 9438 At special positions: 0 Unit cell: (153.34, 112.34, 109.06, 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 59 16.00 O 1718 8.00 N 1625 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 19 sheets defined 32.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 4.255A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 4.130A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.517A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.572A pdb=" N MET A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.699A pdb=" N PHE A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 308 removed outlier: 4.738A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 removed outlier: 3.533A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.726A pdb=" N ALA C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.630A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.640A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.596A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'E' and resid 2 through 27 removed outlier: 4.430A pdb=" N SER E 8 " --> pdb=" O GLY E 4 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 12 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 41 removed outlier: 3.511A pdb=" N GLU R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 118 through 122 removed outlier: 3.632A pdb=" N GLN R 122 " --> pdb=" O SER R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.521A pdb=" N ILE R 128 " --> pdb=" O ASP R 124 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL R 134 " --> pdb=" O VAL R 130 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR R 146 " --> pdb=" O GLN R 142 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU R 158 " --> pdb=" O GLY R 154 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU R 163 " --> pdb=" O ALA R 159 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 182 Processing helix chain 'R' and resid 184 through 197 removed outlier: 3.921A pdb=" N SER R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 216 removed outlier: 3.594A pdb=" N THR R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU R 216 " --> pdb=" O VAL R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 235 removed outlier: 3.824A pdb=" N ALA R 228 " --> pdb=" O CYS R 224 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 253 removed outlier: 3.523A pdb=" N VAL R 244 " --> pdb=" O CYS R 240 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU R 249 " --> pdb=" O GLU R 245 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 removed outlier: 3.641A pdb=" N TYR R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY R 269 " --> pdb=" O SER R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 277 Processing helix chain 'R' and resid 278 through 288 removed outlier: 3.595A pdb=" N LEU R 288 " --> pdb=" O VAL R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 308 through 330 removed outlier: 3.715A pdb=" N ILE R 315 " --> pdb=" O VAL R 311 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE R 325 " --> pdb=" O ILE R 321 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN R 327 " --> pdb=" O VAL R 323 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU R 329 " --> pdb=" O ILE R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 333 No H-bonds generated for 'chain 'R' and resid 331 through 333' Processing helix chain 'R' and resid 334 through 338 removed outlier: 3.776A pdb=" N GLN R 337 " --> pdb=" O ARG R 334 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N MET R 338 " --> pdb=" O ALA R 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 334 through 338' Processing helix chain 'R' and resid 340 through 344 removed outlier: 3.545A pdb=" N TYR R 343 " --> pdb=" O HIS R 340 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS R 344 " --> pdb=" O THR R 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 340 through 344' Processing helix chain 'R' and resid 345 through 350 Processing helix chain 'R' and resid 375 through 403 removed outlier: 3.874A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU R 382 " --> pdb=" O ARG R 378 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE R 383 " --> pdb=" O SER R 379 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU R 386 " --> pdb=" O LEU R 382 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL R 396 " --> pdb=" O GLN R 392 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR R 400 " --> pdb=" O VAL R 396 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU R 403 " --> pdb=" O LEU R 399 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 418 removed outlier: 3.586A pdb=" N ARG R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.207A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.592A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 113 removed outlier: 6.023A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.894A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.453A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.560A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.523A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 328 through 329 removed outlier: 3.689A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.006A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR D 115 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 59 through 60 removed outlier: 4.165A pdb=" N TYR D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 148 removed outlier: 6.510A pdb=" N VAL D 147 " --> pdb=" O GLU D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 155 through 159 removed outlier: 3.666A pdb=" N SER D 206 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 177 through 179 Processing sheet with id=AB9, first strand: chain 'D' and resid 189 through 190 Processing sheet with id=AC1, first strand: chain 'R' and resid 79 through 80 removed outlier: 4.097A pdb=" N ILE R 79 " --> pdb=" O VAL R 96 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 762 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: 2.46 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3020 1.34 - 1.46: 2422 1.46 - 1.58: 4144 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9666 Sorted by residual: bond pdb=" C ILE R 355 " pdb=" N PRO R 356 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.47e+00 bond pdb=" C TRP B 99 " pdb=" N VAL B 100 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.29e-02 6.01e+03 4.49e+00 bond pdb=" N THR R 257 " pdb=" CA THR R 257 " ideal model delta sigma weight residual 1.460 1.485 -0.025 1.54e-02 4.22e+03 2.74e+00 bond pdb=" CB ASN R 238 " pdb=" CG ASN R 238 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.42e+00 bond pdb=" CA ASN R 238 " pdb=" CB ASN R 238 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.45e-02 4.76e+03 2.23e+00 ... (remaining 9661 not shown) Histogram of bond angle deviations from ideal: 98.96 - 106.01: 153 106.01 - 113.06: 5169 113.06 - 120.11: 3537 120.11 - 127.15: 4131 127.15 - 134.20: 138 Bond angle restraints: 13128 Sorted by residual: angle pdb=" N VAL R 191 " pdb=" CA VAL R 191 " pdb=" C VAL R 191 " ideal model delta sigma weight residual 112.96 106.65 6.31 1.00e+00 1.00e+00 3.98e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 122.46 129.03 -6.57 1.41e+00 5.03e-01 2.17e+01 angle pdb=" C VAL R 368 " pdb=" N THR R 369 " pdb=" CA THR R 369 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N VAL R 236 " pdb=" CA VAL R 236 " pdb=" C VAL R 236 " ideal model delta sigma weight residual 113.53 109.12 4.41 9.80e-01 1.04e+00 2.02e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 ... (remaining 13123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 4893 17.10 - 34.21: 597 34.21 - 51.31: 126 51.31 - 68.41: 13 68.41 - 85.52: 7 Dihedral angle restraints: 5636 sinusoidal: 2115 harmonic: 3521 Sorted by residual: dihedral pdb=" CA PRO R 356 " pdb=" C PRO R 356 " pdb=" N LEU R 357 " pdb=" CA LEU R 357 " ideal model delta harmonic sigma weight residual 180.00 140.63 39.37 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CA VAL R 292 " pdb=" C VAL R 292 " pdb=" N GLN R 293 " pdb=" CA GLN R 293 " ideal model delta harmonic sigma weight residual 180.00 -144.91 -35.09 0 5.00e+00 4.00e-02 4.93e+01 dihedral pdb=" CA GLY B 77 " pdb=" C GLY B 77 " pdb=" N LYS B 78 " pdb=" CA LYS B 78 " ideal model delta harmonic sigma weight residual -180.00 -151.84 -28.16 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 5633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1128 0.062 - 0.123: 290 0.123 - 0.185: 40 0.185 - 0.246: 6 0.246 - 0.307: 3 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CB VAL R 91 " pdb=" CA VAL R 91 " pdb=" CG1 VAL R 91 " pdb=" CG2 VAL R 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE D 100 " pdb=" CA ILE D 100 " pdb=" CG1 ILE D 100 " pdb=" CG2 ILE D 100 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1464 not shown) Planarity restraints: 1661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.031 2.00e-02 2.50e+03 2.23e-02 9.97e+00 pdb=" CG TYR B 59 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 355 " 0.042 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO R 356 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 356 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 356 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 184 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO D 185 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 185 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 185 " -0.034 5.00e-02 4.00e+02 ... (remaining 1658 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2621 2.79 - 3.32: 8200 3.32 - 3.84: 15594 3.84 - 4.37: 17849 4.37 - 4.90: 30125 Nonbonded interactions: 74389 Sorted by model distance: nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.260 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.270 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.276 2.440 nonbonded pdb=" O SER R 183 " pdb=" OG SER R 183 " model vdw 2.296 2.440 ... (remaining 74384 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.930 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.580 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9666 Z= 0.413 Angle : 0.959 13.638 13128 Z= 0.539 Chirality : 0.055 0.307 1467 Planarity : 0.006 0.065 1661 Dihedral : 15.401 85.516 3355 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.51 % Allowed : 14.69 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.53 (0.18), residues: 1203 helix: -4.57 (0.11), residues: 373 sheet: -3.27 (0.28), residues: 247 loop : -3.13 (0.22), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 258 HIS 0.010 0.002 HIS R 250 PHE 0.026 0.002 PHE R 264 TYR 0.054 0.002 TYR B 59 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 209 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 212 average time/residue: 0.2613 time to fit residues: 73.2441 Evaluate side-chains 144 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0885 time to fit residues: 1.7615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 62 HIS B 142 HIS B 266 HIS D 13 GLN D 77 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 HIS ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN R 250 HIS R 408 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9666 Z= 0.182 Angle : 0.616 8.723 13128 Z= 0.325 Chirality : 0.041 0.159 1467 Planarity : 0.005 0.054 1661 Dihedral : 6.007 35.903 1317 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.94 % Allowed : 18.54 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.20), residues: 1203 helix: -3.19 (0.19), residues: 368 sheet: -2.72 (0.30), residues: 241 loop : -2.72 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.006 0.001 HIS B 266 PHE 0.016 0.001 PHE A 191 TYR 0.017 0.001 TYR R 145 ARG 0.006 0.000 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 188 average time/residue: 0.2198 time to fit residues: 57.5269 Evaluate side-chains 152 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0891 time to fit residues: 3.4597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 91 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 361 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 9666 Z= 0.435 Angle : 0.734 7.431 13128 Z= 0.391 Chirality : 0.047 0.198 1467 Planarity : 0.005 0.056 1661 Dihedral : 6.483 38.306 1317 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 4.46 % Allowed : 23.71 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.92 (0.22), residues: 1203 helix: -2.52 (0.22), residues: 370 sheet: -2.52 (0.33), residues: 217 loop : -2.66 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS D 232 PHE 0.026 0.002 PHE R 264 TYR 0.032 0.002 TYR R 145 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 27 residues processed: 180 average time/residue: 0.1999 time to fit residues: 51.5981 Evaluate side-chains 160 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0952 time to fit residues: 6.1723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN E 3 GLN ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9666 Z= 0.193 Angle : 0.593 8.598 13128 Z= 0.311 Chirality : 0.041 0.159 1467 Planarity : 0.004 0.052 1661 Dihedral : 5.828 46.185 1317 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.33 % Allowed : 26.44 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.22), residues: 1203 helix: -2.04 (0.24), residues: 368 sheet: -2.41 (0.30), residues: 249 loop : -2.46 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 372 PHE 0.016 0.001 PHE R 365 TYR 0.014 0.001 TYR R 145 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 168 average time/residue: 0.2164 time to fit residues: 51.5152 Evaluate side-chains 148 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0983 time to fit residues: 3.6055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 79 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 103 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9666 Z= 0.169 Angle : 0.589 8.879 13128 Z= 0.304 Chirality : 0.041 0.155 1467 Planarity : 0.003 0.045 1661 Dihedral : 5.497 48.039 1317 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.72 % Allowed : 27.36 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.23), residues: 1203 helix: -1.55 (0.26), residues: 366 sheet: -2.22 (0.31), residues: 245 loop : -2.27 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 111 HIS 0.004 0.001 HIS R 177 PHE 0.017 0.001 PHE B 253 TYR 0.015 0.001 TYR R 145 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 160 average time/residue: 0.2174 time to fit residues: 49.3630 Evaluate side-chains 138 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0946 time to fit residues: 2.2751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.0020 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 GLN ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN R 361 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9666 Z= 0.154 Angle : 0.581 9.147 13128 Z= 0.296 Chirality : 0.041 0.161 1467 Planarity : 0.003 0.045 1661 Dihedral : 5.213 51.171 1317 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.62 % Allowed : 28.06 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.74 (0.23), residues: 1203 helix: -1.16 (0.26), residues: 368 sheet: -1.89 (0.33), residues: 243 loop : -2.18 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.000 HIS R 372 PHE 0.036 0.001 PHE D 68 TYR 0.017 0.001 TYR R 145 ARG 0.003 0.000 ARG R 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 164 average time/residue: 0.2216 time to fit residues: 51.0271 Evaluate side-chains 134 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1004 time to fit residues: 2.8475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 84 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9666 Z= 0.264 Angle : 0.633 7.442 13128 Z= 0.327 Chirality : 0.043 0.173 1467 Planarity : 0.004 0.045 1661 Dihedral : 5.512 51.608 1317 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.72 % Allowed : 29.69 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.75 (0.23), residues: 1203 helix: -1.22 (0.26), residues: 367 sheet: -1.86 (0.33), residues: 244 loop : -2.17 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 36 HIS 0.005 0.001 HIS A 213 PHE 0.019 0.002 PHE B 253 TYR 0.021 0.001 TYR R 145 ARG 0.006 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 145 average time/residue: 0.2256 time to fit residues: 45.8148 Evaluate side-chains 139 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0912 time to fit residues: 2.9470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9666 Z= 0.222 Angle : 0.622 7.908 13128 Z= 0.320 Chirality : 0.042 0.166 1467 Planarity : 0.003 0.046 1661 Dihedral : 5.387 53.400 1317 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.01 % Allowed : 29.38 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.56 (0.24), residues: 1203 helix: -1.06 (0.26), residues: 366 sheet: -1.69 (0.33), residues: 244 loop : -2.08 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.020 0.001 PHE E 22 TYR 0.022 0.001 TYR R 145 ARG 0.006 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 141 average time/residue: 0.2360 time to fit residues: 46.7634 Evaluate side-chains 133 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0920 time to fit residues: 2.3965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 0.0980 chunk 68 optimal weight: 10.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9666 Z= 0.161 Angle : 0.594 8.538 13128 Z= 0.302 Chirality : 0.041 0.161 1467 Planarity : 0.003 0.045 1661 Dihedral : 5.061 53.451 1317 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.51 % Allowed : 30.19 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.24), residues: 1203 helix: -0.70 (0.27), residues: 369 sheet: -1.51 (0.34), residues: 242 loop : -1.96 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.021 0.001 PHE E 22 TYR 0.016 0.001 TYR R 145 ARG 0.006 0.000 ARG R 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 139 average time/residue: 0.2242 time to fit residues: 43.8903 Evaluate side-chains 133 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0888 time to fit residues: 2.1236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 57 optimal weight: 0.0040 chunk 74 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9666 Z= 0.175 Angle : 0.614 8.719 13128 Z= 0.309 Chirality : 0.041 0.164 1467 Planarity : 0.003 0.044 1661 Dihedral : 4.984 49.798 1317 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.61 % Allowed : 29.89 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.13 (0.24), residues: 1203 helix: -0.51 (0.27), residues: 365 sheet: -1.46 (0.35), residues: 234 loop : -1.96 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.026 0.001 PHE E 22 TYR 0.016 0.001 TYR R 145 ARG 0.005 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 139 average time/residue: 0.2348 time to fit residues: 45.7422 Evaluate side-chains 129 residues out of total 1047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1026 time to fit residues: 1.7901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.115934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089135 restraints weight = 20216.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090060 restraints weight = 14778.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090786 restraints weight = 11265.115| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9666 Z= 0.193 Angle : 0.620 9.832 13128 Z= 0.314 Chirality : 0.042 0.167 1467 Planarity : 0.003 0.060 1661 Dihedral : 4.989 46.830 1317 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.41 % Allowed : 30.50 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.24), residues: 1203 helix: -0.38 (0.28), residues: 360 sheet: -1.39 (0.34), residues: 239 loop : -1.91 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 PHE 0.022 0.001 PHE E 22 TYR 0.017 0.001 TYR R 145 ARG 0.009 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.61 seconds wall clock time: 39 minutes 2.13 seconds (2342.13 seconds total)