Starting phenix.real_space_refine on Mon Mar 11 14:47:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/03_2024/7vvk_32142.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/03_2024/7vvk_32142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/03_2024/7vvk_32142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/03_2024/7vvk_32142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/03_2024/7vvk_32142.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/03_2024/7vvk_32142.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 52 5.16 5 C 5405 2.51 5 N 1485 2.21 5 O 1574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8516 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1903 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2544 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 396 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 965 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE%COO:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2457 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 6, 'TRANS': 327} Chain breaks: 6 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 238 Time building chain proxies: 4.91, per 1000 atoms: 0.58 Number of scatterers: 8516 At special positions: 0 Unit cell: (127.267, 99.6003, 122.84, 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 52 16.00 O 1574 8.00 N 1485 7.00 C 5405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.00 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 41.7% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.639A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.573A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.509A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.521A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.573A pdb=" N GLU A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.984A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.974A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.509A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.616A pdb=" N HIS A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.566A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.643A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 44 removed outlier: 3.878A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.659A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 removed outlier: 3.541A pdb=" N GLN P 29 " --> pdb=" O ARG P 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 180 through 212 removed outlier: 4.114A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU R 187 " --> pdb=" O VAL R 183 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET R 189 " --> pdb=" O ASP R 185 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE R 190 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 246 removed outlier: 3.783A pdb=" N ILE R 237 " --> pdb=" O ARG R 233 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 4.232A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 346 removed outlier: 3.907A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU R 346 " --> pdb=" O VAL R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.839A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 removed outlier: 3.620A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.898A pdb=" N SER R 370 " --> pdb=" O PRO R 366 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE R 371 " --> pdb=" O ILE R 367 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL R 372 " --> pdb=" O LEU R 368 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN R 374 " --> pdb=" O SER R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 420 through 424 removed outlier: 3.515A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 449 Processing helix chain 'R' and resid 450 through 461 Processing helix chain 'R' and resid 463 through 478 removed outlier: 3.826A pdb=" N GLU R 469 " --> pdb=" O GLU R 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 9.371A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.670A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.040A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.694A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.096A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.698A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.377A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.779A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.508A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 128 through 130 408 hydrogen bonds defined for protein. 1167 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: 2.29 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1441 1.31 - 1.45: 2405 1.45 - 1.59: 4766 1.59 - 1.73: 0 1.73 - 1.87: 76 Bond restraints: 8688 Sorted by residual: bond pdb=" C ARG B 314 " pdb=" O ARG B 314 " ideal model delta sigma weight residual 1.234 1.304 -0.069 1.20e-02 6.94e+03 3.34e+01 bond pdb=" CE1 HIS R 307 " pdb=" NE2 HIS R 307 " ideal model delta sigma weight residual 1.321 1.376 -0.055 1.00e-02 1.00e+04 3.00e+01 bond pdb=" C SER B 189 " pdb=" O SER B 189 " ideal model delta sigma weight residual 1.234 1.172 0.061 1.24e-02 6.50e+03 2.44e+01 bond pdb=" C ILE B 338 " pdb=" O ILE B 338 " ideal model delta sigma weight residual 1.237 1.185 0.051 1.07e-02 8.73e+03 2.31e+01 bond pdb=" N ILE R 115 " pdb=" CA ILE R 115 " ideal model delta sigma weight residual 1.458 1.498 -0.041 9.00e-03 1.23e+04 2.03e+01 ... (remaining 8683 not shown) Histogram of bond angle deviations from ideal: 95.20 - 103.23: 54 103.23 - 111.26: 2926 111.26 - 119.29: 4967 119.29 - 127.32: 3755 127.32 - 135.34: 97 Bond angle restraints: 11799 Sorted by residual: angle pdb=" N ILE R 371 " pdb=" CA ILE R 371 " pdb=" C ILE R 371 " ideal model delta sigma weight residual 111.81 106.43 5.38 8.60e-01 1.35e+00 3.92e+01 angle pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " ideal model delta sigma weight residual 112.60 118.42 -5.82 1.00e+00 1.00e+00 3.38e+01 angle pdb=" C THR A 315 " pdb=" CA THR A 315 " pdb=" CB THR A 315 " ideal model delta sigma weight residual 110.33 115.59 -5.26 1.02e+00 9.61e-01 2.66e+01 angle pdb=" N ARG N 67 " pdb=" CA ARG N 67 " pdb=" C ARG N 67 " ideal model delta sigma weight residual 113.55 107.10 6.45 1.26e+00 6.30e-01 2.62e+01 angle pdb=" C SER R 433 " pdb=" N GLY R 434 " pdb=" CA GLY R 434 " ideal model delta sigma weight residual 119.92 124.81 -4.89 9.60e-01 1.09e+00 2.60e+01 ... (remaining 11794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4672 17.99 - 35.97: 365 35.97 - 53.96: 57 53.96 - 71.95: 13 71.95 - 89.93: 6 Dihedral angle restraints: 5113 sinusoidal: 1854 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 136.96 -43.96 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N ARG A 232 " pdb=" CA ARG A 232 " ideal model delta harmonic sigma weight residual 180.00 -156.49 -23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 750 0.068 - 0.137: 445 0.137 - 0.205: 127 0.205 - 0.273: 21 0.273 - 0.342: 2 Chirality restraints: 1345 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB VAL P 31 " pdb=" CA VAL P 31 " pdb=" CG1 VAL P 31 " pdb=" CG2 VAL P 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA VAL A 277 " pdb=" N VAL A 277 " pdb=" C VAL A 277 " pdb=" CB VAL A 277 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1342 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.064 2.00e-02 2.50e+03 3.11e-02 2.42e+01 pdb=" CG TRP A 271 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 329 " -0.047 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP R 329 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP R 329 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP R 329 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP R 329 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP R 329 " -0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP R 329 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 329 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 329 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP R 329 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " -0.060 2.00e-02 2.50e+03 2.79e-02 1.94e+01 pdb=" CG TRP B 99 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " -0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " -0.019 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 743 2.76 - 3.29: 8851 3.29 - 3.83: 13479 3.83 - 4.36: 17823 4.36 - 4.90: 29238 Nonbonded interactions: 70134 Sorted by model distance: nonbonded pdb=" O LEU A 383 " pdb=" OG SER R 409 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.250 2.440 nonbonded pdb=" O ALA R 344 " pdb=" ND2 ASN R 348 " model vdw 2.262 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O GLY B 288 " model vdw 2.264 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.282 2.440 ... (remaining 70129 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: 0.090 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: 0.000 Extract box with map and model: 1.100 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.830 Find NCS groups from input model: 0.200 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 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 : 0.015 0.091 8688 Z= 0.971 Angle : 1.746 7.111 11799 Z= 1.274 Chirality : 0.087 0.342 1345 Planarity : 0.008 0.038 1511 Dihedral : 13.866 89.932 2992 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.20 % Favored : 95.62 % Rotamer: Outliers : 0.47 % Allowed : 4.47 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.24), residues: 1095 helix: -0.30 (0.24), residues: 422 sheet: -0.46 (0.39), residues: 189 loop : -0.80 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.011 TRP A 271 HIS 0.027 0.006 HIS P 9 PHE 0.048 0.009 PHE A 246 TYR 0.057 0.010 TYR R 297 ARG 0.027 0.003 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7300 (tmmt) cc_final: 0.7097 (tptt) REVERT: A 28 LYS cc_start: 0.6888 (mmpt) cc_final: 0.6513 (ptmm) REVERT: A 32 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6958 (mttm) REVERT: A 253 TYR cc_start: 0.7739 (m-80) cc_final: 0.7518 (m-80) REVERT: A 255 ARG cc_start: 0.6954 (mtp-110) cc_final: 0.6746 (ttm170) REVERT: A 273 ARG cc_start: 0.6823 (ptp-110) cc_final: 0.6585 (ptp-170) REVERT: A 297 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7437 (mtpp) REVERT: A 337 ARG cc_start: 0.7152 (tmt-80) cc_final: 0.6668 (ttm-80) REVERT: A 342 SER cc_start: 0.5333 (p) cc_final: 0.5119 (m) REVERT: B 119 ASN cc_start: 0.7894 (m110) cc_final: 0.7644 (m110) REVERT: B 145 TYR cc_start: 0.8202 (p90) cc_final: 0.7656 (p90) REVERT: B 152 LEU cc_start: 0.8092 (mt) cc_final: 0.7716 (mp) REVERT: B 156 GLN cc_start: 0.7582 (mm110) cc_final: 0.7233 (mt0) REVERT: B 184 THR cc_start: 0.7165 (p) cc_final: 0.6880 (t) REVERT: B 226 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 233 CYS cc_start: 0.8754 (p) cc_final: 0.8276 (t) REVERT: B 239 ASN cc_start: 0.8047 (m-40) cc_final: 0.7651 (m-40) REVERT: B 254 ASP cc_start: 0.7230 (t0) cc_final: 0.6990 (t0) REVERT: B 262 MET cc_start: 0.7388 (ttt) cc_final: 0.7018 (tpp) REVERT: B 291 ASP cc_start: 0.6989 (t70) cc_final: 0.6759 (t0) REVERT: B 298 ASP cc_start: 0.8670 (t0) cc_final: 0.8456 (t70) REVERT: B 301 LYS cc_start: 0.6862 (mmtt) cc_final: 0.6606 (mmtt) REVERT: B 314 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6551 (ttm170) REVERT: B 322 ASP cc_start: 0.7216 (m-30) cc_final: 0.6823 (m-30) REVERT: B 337 LYS cc_start: 0.8292 (mttt) cc_final: 0.8059 (mttm) REVERT: G 38 MET cc_start: 0.6732 (tpt) cc_final: 0.6449 (ttp) REVERT: G 46 LYS cc_start: 0.6996 (mppt) cc_final: 0.6713 (tptp) REVERT: N 34 MET cc_start: 0.8449 (mmm) cc_final: 0.8016 (mmm) REVERT: N 105 ARG cc_start: 0.6339 (mmt-90) cc_final: 0.5470 (mtp180) REVERT: N 117 TYR cc_start: 0.7447 (m-80) cc_final: 0.6866 (m-80) REVERT: N 120 GLN cc_start: 0.7032 (tt0) cc_final: 0.6696 (mm110) REVERT: R 224 MET cc_start: 0.6862 (mmm) cc_final: 0.6352 (ttm) REVERT: R 311 PHE cc_start: 0.7180 (m-80) cc_final: 0.6687 (m-80) REVERT: R 312 MET cc_start: 0.7240 (mmm) cc_final: 0.6861 (mtp) REVERT: R 315 PHE cc_start: 0.3986 (t80) cc_final: 0.3634 (t80) REVERT: R 429 TYR cc_start: 0.3934 (m-10) cc_final: 0.3453 (m-80) REVERT: R 458 ILE cc_start: 0.6587 (mt) cc_final: 0.6212 (mm) REVERT: R 474 TRP cc_start: 0.5888 (t60) cc_final: 0.5640 (t60) outliers start: 4 outliers final: 0 residues processed: 224 average time/residue: 0.2837 time to fit residues: 81.0222 Evaluate side-chains 162 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 176 GLN B 313 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN P 29 GLN R 223 HIS ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8688 Z= 0.200 Angle : 0.549 6.974 11799 Z= 0.297 Chirality : 0.043 0.228 1345 Planarity : 0.004 0.037 1511 Dihedral : 4.414 29.993 1208 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.23 % Allowed : 10.81 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1095 helix: 1.16 (0.25), residues: 430 sheet: -0.31 (0.36), residues: 214 loop : -0.38 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 298 HIS 0.006 0.001 HIS P 9 PHE 0.022 0.001 PHE R 335 TYR 0.017 0.002 TYR R 297 ARG 0.004 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 297 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7417 (mtpp) REVERT: A 336 LEU cc_start: 0.8008 (mt) cc_final: 0.7754 (mt) REVERT: A 337 ARG cc_start: 0.7176 (tmt-80) cc_final: 0.6716 (ttm110) REVERT: A 342 SER cc_start: 0.5475 (p) cc_final: 0.5096 (m) REVERT: A 357 VAL cc_start: 0.6840 (p) cc_final: 0.6532 (t) REVERT: A 381 TYR cc_start: 0.6973 (m-80) cc_final: 0.6658 (m-80) REVERT: B 44 GLN cc_start: 0.6603 (pm20) cc_final: 0.6294 (pm20) REVERT: B 59 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: B 145 TYR cc_start: 0.8176 (p90) cc_final: 0.7529 (p90) REVERT: B 152 LEU cc_start: 0.8123 (mt) cc_final: 0.7774 (mp) REVERT: B 226 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 233 CYS cc_start: 0.8600 (p) cc_final: 0.8180 (t) REVERT: B 239 ASN cc_start: 0.7754 (m-40) cc_final: 0.7367 (m-40) REVERT: B 271 CYS cc_start: 0.7262 (m) cc_final: 0.6579 (p) REVERT: B 322 ASP cc_start: 0.7090 (m-30) cc_final: 0.6740 (m-30) REVERT: B 325 MET cc_start: 0.7052 (tpp) cc_final: 0.6767 (tpp) REVERT: N 34 MET cc_start: 0.8129 (mmm) cc_final: 0.7848 (mmm) REVERT: N 105 ARG cc_start: 0.6270 (mmt-90) cc_final: 0.5497 (mtp180) REVERT: N 117 TYR cc_start: 0.7026 (m-80) cc_final: 0.6467 (m-80) REVERT: N 120 GLN cc_start: 0.6996 (tt0) cc_final: 0.6694 (mm-40) REVERT: R 206 VAL cc_start: 0.6206 (t) cc_final: 0.6005 (t) REVERT: R 224 MET cc_start: 0.6821 (mmm) cc_final: 0.6518 (ttm) REVERT: R 315 PHE cc_start: 0.4320 (t80) cc_final: 0.4026 (t80) REVERT: R 429 TYR cc_start: 0.3632 (m-10) cc_final: 0.3385 (m-80) REVERT: R 458 ILE cc_start: 0.6217 (mt) cc_final: 0.5845 (mp) REVERT: R 474 TRP cc_start: 0.5721 (t60) cc_final: 0.4641 (t-100) outliers start: 19 outliers final: 10 residues processed: 189 average time/residue: 0.2468 time to fit residues: 60.9941 Evaluate side-chains 155 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.0570 chunk 83 optimal weight: 40.0000 chunk 68 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.0370 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 overall best weight: 0.8116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 176 GLN B 313 ASN B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8688 Z= 0.146 Angle : 0.479 5.122 11799 Z= 0.261 Chirality : 0.041 0.210 1345 Planarity : 0.003 0.040 1511 Dihedral : 4.103 23.982 1208 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.00 % Allowed : 14.57 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1095 helix: 1.68 (0.25), residues: 432 sheet: -0.29 (0.35), residues: 227 loop : -0.29 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.017 0.001 TYR R 191 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 297 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7391 (mtpp) REVERT: A 337 ARG cc_start: 0.7237 (tmt-80) cc_final: 0.6833 (ttm110) REVERT: A 381 TYR cc_start: 0.6955 (m-80) cc_final: 0.6668 (m-80) REVERT: B 17 GLN cc_start: 0.6493 (tm-30) cc_final: 0.6206 (tm-30) REVERT: B 37 ILE cc_start: 0.5481 (tt) cc_final: 0.5253 (tt) REVERT: B 44 GLN cc_start: 0.6520 (pm20) cc_final: 0.6223 (pm20) REVERT: B 145 TYR cc_start: 0.8200 (p90) cc_final: 0.7631 (p90) REVERT: B 152 LEU cc_start: 0.7998 (mt) cc_final: 0.7716 (mp) REVERT: B 215 GLU cc_start: 0.6663 (tp30) cc_final: 0.6117 (mm-30) REVERT: B 226 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 239 ASN cc_start: 0.7961 (m-40) cc_final: 0.7506 (m-40) REVERT: B 262 MET cc_start: 0.7492 (tpp) cc_final: 0.7233 (tpp) REVERT: B 313 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6952 (m-40) REVERT: B 325 MET cc_start: 0.7019 (tpp) cc_final: 0.6619 (tpp) REVERT: G 21 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4741 (ttm) REVERT: N 34 MET cc_start: 0.8063 (mmm) cc_final: 0.7783 (mmm) REVERT: N 91 THR cc_start: 0.6766 (t) cc_final: 0.6316 (m) REVERT: N 105 ARG cc_start: 0.6160 (mmt-90) cc_final: 0.5413 (mtp180) REVERT: N 117 TYR cc_start: 0.7090 (m-80) cc_final: 0.6455 (m-80) REVERT: N 120 GLN cc_start: 0.6870 (tt0) cc_final: 0.6623 (mm-40) REVERT: R 206 VAL cc_start: 0.6523 (t) cc_final: 0.6271 (t) REVERT: R 224 MET cc_start: 0.6931 (mmm) cc_final: 0.6501 (ttp) REVERT: R 231 MET cc_start: 0.5460 (mmt) cc_final: 0.5250 (mmt) REVERT: R 315 PHE cc_start: 0.4262 (t80) cc_final: 0.4014 (t80) REVERT: R 458 ILE cc_start: 0.6163 (mt) cc_final: 0.5849 (mp) outliers start: 17 outliers final: 13 residues processed: 174 average time/residue: 0.2407 time to fit residues: 55.9505 Evaluate side-chains 154 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN N 35 ASN P 14 HIS R 295 ASN R 442 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8688 Z= 0.280 Angle : 0.572 6.118 11799 Z= 0.309 Chirality : 0.044 0.258 1345 Planarity : 0.004 0.044 1511 Dihedral : 4.529 25.689 1208 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.00 % Allowed : 15.98 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1095 helix: 1.50 (0.25), residues: 430 sheet: -0.30 (0.36), residues: 227 loop : -0.51 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.007 0.002 HIS P 9 PHE 0.021 0.002 PHE A 212 TYR 0.026 0.002 TYR R 297 ARG 0.004 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 ARG cc_start: 0.7227 (tmt-80) cc_final: 0.6731 (ttm110) REVERT: B 17 GLN cc_start: 0.6464 (tm-30) cc_final: 0.6174 (tm-30) REVERT: B 44 GLN cc_start: 0.6603 (pm20) cc_final: 0.6297 (pm20) REVERT: B 59 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: B 152 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7417 (mt) REVERT: B 158 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7087 (m) REVERT: B 226 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7534 (mt-10) REVERT: B 262 MET cc_start: 0.7805 (tpp) cc_final: 0.7592 (tpp) REVERT: N 7 SER cc_start: 0.6072 (t) cc_final: 0.5498 (p) REVERT: N 34 MET cc_start: 0.7897 (mmm) cc_final: 0.7695 (mmm) REVERT: N 91 THR cc_start: 0.6693 (t) cc_final: 0.6248 (m) REVERT: N 105 ARG cc_start: 0.6330 (mmt-90) cc_final: 0.5645 (mtp180) REVERT: N 117 TYR cc_start: 0.7295 (m-80) cc_final: 0.6718 (m-80) REVERT: N 120 GLN cc_start: 0.6877 (tt0) cc_final: 0.6655 (mm110) REVERT: R 206 VAL cc_start: 0.6452 (t) cc_final: 0.6152 (t) REVERT: R 224 MET cc_start: 0.7009 (mmm) cc_final: 0.6752 (ttp) REVERT: R 302 GLU cc_start: 0.7561 (tt0) cc_final: 0.7361 (tt0) REVERT: R 331 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6773 (tt) REVERT: R 458 ILE cc_start: 0.6256 (mt) cc_final: 0.5968 (mp) outliers start: 34 outliers final: 22 residues processed: 169 average time/residue: 0.2273 time to fit residues: 51.2414 Evaluate side-chains 165 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8688 Z= 0.304 Angle : 0.582 6.236 11799 Z= 0.315 Chirality : 0.045 0.263 1345 Planarity : 0.004 0.045 1511 Dihedral : 4.737 27.631 1208 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.35 % Allowed : 17.04 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1095 helix: 1.34 (0.25), residues: 425 sheet: -0.30 (0.35), residues: 223 loop : -0.87 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.005 0.002 HIS P 9 PHE 0.023 0.002 PHE A 212 TYR 0.017 0.002 TYR R 191 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: A 337 ARG cc_start: 0.7138 (tmt-80) cc_final: 0.6648 (ttm110) REVERT: B 44 GLN cc_start: 0.6576 (pm20) cc_final: 0.6268 (pm20) REVERT: B 59 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: B 87 THR cc_start: 0.7818 (m) cc_final: 0.7234 (p) REVERT: B 152 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7633 (mp) REVERT: B 219 ARG cc_start: 0.7480 (ptp-110) cc_final: 0.6531 (mtp180) REVERT: B 226 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 259 GLN cc_start: 0.7972 (pm20) cc_final: 0.7672 (pm20) REVERT: B 313 ASN cc_start: 0.7233 (OUTLIER) cc_final: 0.6889 (m-40) REVERT: B 336 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8026 (tt) REVERT: N 7 SER cc_start: 0.5922 (t) cc_final: 0.5354 (p) REVERT: N 105 ARG cc_start: 0.6521 (mmt-90) cc_final: 0.5800 (mtp180) REVERT: N 117 TYR cc_start: 0.7511 (m-80) cc_final: 0.7153 (m-80) REVERT: N 120 GLN cc_start: 0.6921 (tt0) cc_final: 0.6679 (mm-40) REVERT: R 206 VAL cc_start: 0.6547 (t) cc_final: 0.6225 (t) REVERT: R 224 MET cc_start: 0.6894 (mmm) cc_final: 0.6626 (ttp) REVERT: R 302 GLU cc_start: 0.7588 (tt0) cc_final: 0.7382 (tt0) REVERT: R 331 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6714 (tt) REVERT: R 443 TYR cc_start: 0.5748 (OUTLIER) cc_final: 0.5297 (t80) REVERT: R 458 ILE cc_start: 0.6247 (mt) cc_final: 0.5968 (mp) outliers start: 37 outliers final: 24 residues processed: 171 average time/residue: 0.2389 time to fit residues: 54.1563 Evaluate side-chains 164 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 443 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN B 88 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8688 Z= 0.260 Angle : 0.555 8.518 11799 Z= 0.297 Chirality : 0.043 0.260 1345 Planarity : 0.004 0.045 1511 Dihedral : 4.624 28.412 1208 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.05 % Allowed : 18.92 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1095 helix: 1.44 (0.25), residues: 422 sheet: -0.30 (0.35), residues: 223 loop : -0.94 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 298 HIS 0.005 0.001 HIS P 9 PHE 0.020 0.002 PHE A 212 TYR 0.016 0.002 TYR R 191 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: A 337 ARG cc_start: 0.7131 (tmt-80) cc_final: 0.6637 (ttm110) REVERT: B 44 GLN cc_start: 0.6547 (pm20) cc_final: 0.6251 (pm20) REVERT: B 59 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6989 (m-80) REVERT: B 152 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7733 (mp) REVERT: B 219 ARG cc_start: 0.7331 (ptp-110) cc_final: 0.6902 (mtp85) REVERT: B 226 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 313 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7199 (m-40) REVERT: B 336 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7986 (tt) REVERT: N 7 SER cc_start: 0.5973 (t) cc_final: 0.5422 (p) REVERT: N 105 ARG cc_start: 0.6324 (mmt-90) cc_final: 0.5620 (mtp180) REVERT: N 117 TYR cc_start: 0.7479 (m-80) cc_final: 0.7081 (m-80) REVERT: N 120 GLN cc_start: 0.6837 (tt0) cc_final: 0.6622 (mm-40) REVERT: R 206 VAL cc_start: 0.6508 (t) cc_final: 0.6176 (t) REVERT: R 224 MET cc_start: 0.6937 (mmm) cc_final: 0.6673 (ttp) REVERT: R 302 GLU cc_start: 0.7565 (tt0) cc_final: 0.7357 (tt0) REVERT: R 331 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6701 (tt) REVERT: R 443 TYR cc_start: 0.5781 (OUTLIER) cc_final: 0.5322 (t80) REVERT: R 458 ILE cc_start: 0.6236 (mt) cc_final: 0.5955 (mp) outliers start: 43 outliers final: 29 residues processed: 172 average time/residue: 0.2416 time to fit residues: 54.6779 Evaluate side-chains 176 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 420 HIS Chi-restraints excluded: chain R residue 443 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8688 Z= 0.187 Angle : 0.506 6.724 11799 Z= 0.272 Chirality : 0.041 0.235 1345 Planarity : 0.003 0.046 1511 Dihedral : 4.362 26.493 1208 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.88 % Allowed : 19.86 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1095 helix: 1.70 (0.25), residues: 422 sheet: -0.11 (0.36), residues: 214 loop : -0.89 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 298 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.001 PHE R 335 TYR 0.015 0.001 TYR R 191 ARG 0.002 0.000 ARG R 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6962 (tt0) REVERT: A 337 ARG cc_start: 0.7060 (tmt-80) cc_final: 0.6592 (ttm110) REVERT: B 44 GLN cc_start: 0.6554 (pm20) cc_final: 0.6248 (pm20) REVERT: B 59 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: B 152 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7727 (mp) REVERT: B 192 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 205 ASP cc_start: 0.7822 (p0) cc_final: 0.7583 (p0) REVERT: B 215 GLU cc_start: 0.6606 (tp30) cc_final: 0.6110 (mm-30) REVERT: B 219 ARG cc_start: 0.7303 (ptp-110) cc_final: 0.6642 (mtp180) REVERT: B 313 ASN cc_start: 0.7442 (OUTLIER) cc_final: 0.7167 (m-40) REVERT: N 7 SER cc_start: 0.6002 (t) cc_final: 0.5442 (p) REVERT: N 117 TYR cc_start: 0.7419 (m-80) cc_final: 0.6986 (m-80) REVERT: N 120 GLN cc_start: 0.6883 (tt0) cc_final: 0.6676 (mm-40) REVERT: R 184 PHE cc_start: 0.5495 (m-10) cc_final: 0.4390 (m-80) REVERT: R 206 VAL cc_start: 0.5954 (t) cc_final: 0.5582 (t) REVERT: R 224 MET cc_start: 0.6914 (mmm) cc_final: 0.6452 (tmm) REVERT: R 331 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6724 (tt) REVERT: R 458 ILE cc_start: 0.6220 (mt) cc_final: 0.5930 (mp) outliers start: 33 outliers final: 24 residues processed: 161 average time/residue: 0.2548 time to fit residues: 54.1365 Evaluate side-chains 166 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 0.0020 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8688 Z= 0.130 Angle : 0.464 7.056 11799 Z= 0.249 Chirality : 0.040 0.224 1345 Planarity : 0.003 0.045 1511 Dihedral : 3.961 20.502 1208 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 22.33 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1095 helix: 2.09 (0.26), residues: 423 sheet: -0.20 (0.35), residues: 214 loop : -0.76 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.014 0.001 TYR R 191 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 270 ARG cc_start: 0.7357 (ttt180) cc_final: 0.6750 (tpt-90) REVERT: A 329 TYR cc_start: 0.7942 (m-80) cc_final: 0.6786 (m-80) REVERT: A 337 ARG cc_start: 0.7063 (tmt-80) cc_final: 0.6591 (ttm110) REVERT: B 44 GLN cc_start: 0.6531 (pm20) cc_final: 0.6237 (pm20) REVERT: B 152 LEU cc_start: 0.7830 (mt) cc_final: 0.7593 (mp) REVERT: B 205 ASP cc_start: 0.7722 (p0) cc_final: 0.7303 (p0) REVERT: B 219 ARG cc_start: 0.7187 (ptp-110) cc_final: 0.6491 (mtp180) REVERT: B 313 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.7084 (m-40) REVERT: N 7 SER cc_start: 0.6007 (t) cc_final: 0.5436 (p) REVERT: N 117 TYR cc_start: 0.7311 (m-80) cc_final: 0.6724 (m-80) REVERT: R 184 PHE cc_start: 0.5981 (m-10) cc_final: 0.4811 (m-80) REVERT: R 206 VAL cc_start: 0.5861 (t) cc_final: 0.5530 (t) REVERT: R 224 MET cc_start: 0.6898 (mmm) cc_final: 0.6478 (tmm) REVERT: R 306 LEU cc_start: 0.7833 (tp) cc_final: 0.7590 (tp) REVERT: R 315 PHE cc_start: 0.4391 (t80) cc_final: 0.4121 (t80) REVERT: R 318 LYS cc_start: 0.5525 (mmtp) cc_final: 0.5188 (mmtt) REVERT: R 458 ILE cc_start: 0.6179 (mt) cc_final: 0.5861 (mp) REVERT: R 474 TRP cc_start: 0.5863 (t60) cc_final: 0.5631 (t60) outliers start: 19 outliers final: 13 residues processed: 158 average time/residue: 0.2790 time to fit residues: 58.2444 Evaluate side-chains 150 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 407 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 32 GLN B 88 ASN B 313 ASN P 16 ASN R 420 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8688 Z= 0.340 Angle : 0.628 6.953 11799 Z= 0.331 Chirality : 0.045 0.220 1345 Planarity : 0.004 0.047 1511 Dihedral : 4.671 23.641 1208 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.11 % Allowed : 21.15 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1095 helix: 1.43 (0.25), residues: 425 sheet: -0.38 (0.35), residues: 215 loop : -0.96 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 298 HIS 0.005 0.002 HIS B 266 PHE 0.021 0.002 PHE A 212 TYR 0.026 0.002 TYR R 297 ARG 0.003 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: A 24 LYS cc_start: 0.7129 (tppt) cc_final: 0.6900 (tptt) REVERT: A 337 ARG cc_start: 0.7112 (tmt-80) cc_final: 0.6631 (ttm110) REVERT: B 138 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6821 (mp0) REVERT: B 152 LEU cc_start: 0.7919 (mt) cc_final: 0.7591 (mp) REVERT: B 192 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 205 ASP cc_start: 0.7891 (p0) cc_final: 0.7634 (p0) REVERT: B 219 ARG cc_start: 0.7389 (ptp-110) cc_final: 0.6965 (mtp85) REVERT: B 313 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.7041 (m-40) REVERT: B 314 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6684 (ptm160) REVERT: N 7 SER cc_start: 0.6087 (t) cc_final: 0.5560 (p) REVERT: N 117 TYR cc_start: 0.7515 (m-80) cc_final: 0.7073 (m-80) REVERT: R 184 PHE cc_start: 0.5467 (m-10) cc_final: 0.4415 (m-80) REVERT: R 206 VAL cc_start: 0.5727 (t) cc_final: 0.5203 (t) REVERT: R 213 ARG cc_start: 0.5335 (ptm-80) cc_final: 0.5102 (ptm-80) REVERT: R 224 MET cc_start: 0.6583 (mmm) cc_final: 0.6237 (ptp) REVERT: R 443 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.5353 (t80) REVERT: R 458 ILE cc_start: 0.6270 (mt) cc_final: 0.5987 (mp) outliers start: 35 outliers final: 27 residues processed: 163 average time/residue: 0.2477 time to fit residues: 53.3149 Evaluate side-chains 165 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 443 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 0.0000 overall best weight: 2.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN B 88 ASN B 313 ASN P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8688 Z= 0.224 Angle : 0.553 6.606 11799 Z= 0.293 Chirality : 0.042 0.207 1345 Planarity : 0.004 0.048 1511 Dihedral : 4.467 22.996 1208 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.94 % Allowed : 22.44 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1095 helix: 1.58 (0.25), residues: 426 sheet: -0.32 (0.35), residues: 216 loop : -0.98 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.002 PHE R 315 TYR 0.020 0.001 TYR R 297 ARG 0.003 0.000 ARG R 343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 337 ARG cc_start: 0.7080 (tmt-80) cc_final: 0.6604 (ttm110) REVERT: B 44 GLN cc_start: 0.6534 (pm20) cc_final: 0.6241 (pm20) REVERT: B 138 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6826 (mp0) REVERT: B 152 LEU cc_start: 0.7885 (mt) cc_final: 0.7628 (mp) REVERT: B 192 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7721 (mt) REVERT: B 205 ASP cc_start: 0.7847 (p0) cc_final: 0.7603 (p0) REVERT: B 219 ARG cc_start: 0.7225 (ptp-110) cc_final: 0.6564 (mtp180) REVERT: B 313 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6787 (m-40) REVERT: N 7 SER cc_start: 0.6069 (t) cc_final: 0.5511 (p) REVERT: N 117 TYR cc_start: 0.7485 (m-80) cc_final: 0.7050 (m-80) REVERT: R 184 PHE cc_start: 0.5495 (m-10) cc_final: 0.4437 (m-80) REVERT: R 206 VAL cc_start: 0.5828 (t) cc_final: 0.5430 (t) REVERT: R 224 MET cc_start: 0.6894 (mmm) cc_final: 0.6413 (tmm) REVERT: R 458 ILE cc_start: 0.6267 (mt) cc_final: 0.5952 (mp) outliers start: 25 outliers final: 23 residues processed: 153 average time/residue: 0.2502 time to fit residues: 50.2962 Evaluate side-chains 158 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0980 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.0270 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0000 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129172 restraints weight = 12098.558| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.17 r_work: 0.3474 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8688 Z= 0.140 Angle : 0.487 6.330 11799 Z= 0.260 Chirality : 0.040 0.182 1345 Planarity : 0.003 0.047 1511 Dihedral : 4.050 18.536 1208 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.12 % Allowed : 23.50 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1095 helix: 2.10 (0.26), residues: 422 sheet: -0.31 (0.35), residues: 214 loop : -0.86 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.001 PHE R 335 TYR 0.014 0.001 TYR R 297 ARG 0.008 0.000 ARG R 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.61 seconds wall clock time: 41 minutes 13.16 seconds (2473.16 seconds total)