Starting phenix.real_space_refine on Fri Dec 8 13:41:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/12_2023/7vvk_32142.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/12_2023/7vvk_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_32142/12_2023/7vvk_32142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/12_2023/7vvk_32142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/12_2023/7vvk_32142.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvk_32142/12_2023/7vvk_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.99, per 1000 atoms: 0.59 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: 3.08 Conformation dependent library (CDL) restraints added in 1.7 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: 0.84 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: 2.42 Time building geometry restraints manager: 3.35 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.050 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.570 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- 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 : 0.963 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 224 average time/residue: 0.2637 time to fit residues: 75.7542 Evaluate side-chains 144 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3768 ------------------------------------------------------------------------------- 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: 0.9980 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 176 GLN B 313 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 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: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8688 Z= 0.204 Angle : 0.552 7.900 11799 Z= 0.300 Chirality : 0.044 0.238 1345 Planarity : 0.004 0.036 1511 Dihedral : 4.435 30.802 1208 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.59 % Allowed : 10.93 % Favored : 86.49 % 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: 0.31 (0.26), residues: 1095 helix: 1.21 (0.25), residues: 430 sheet: -0.30 (0.36), residues: 214 loop : -0.42 (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 0.025 0.002 PHE R 315 TYR 0.016 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 178 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.020 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 171 average time/residue: 0.2358 time to fit residues: 53.5925 Evaluate side-chains 144 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0840 time to fit residues: 3.2096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 40.0000 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.0570 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8688 Z= 0.200 Angle : 0.525 5.755 11799 Z= 0.283 Chirality : 0.042 0.164 1345 Planarity : 0.004 0.040 1511 Dihedral : 4.329 25.798 1208 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.29 % Allowed : 16.22 % Favored : 82.49 % 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: 0.50 (0.26), residues: 1095 helix: 1.47 (0.25), residues: 436 sheet: -0.26 (0.36), residues: 217 loop : -0.42 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 297 HIS 0.007 0.002 HIS A 220 PHE 0.017 0.002 PHE R 335 TYR 0.018 0.002 TYR R 297 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 164 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 1.251 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 162 average time/residue: 0.2454 time to fit residues: 53.3616 Evaluate side-chains 137 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0794 time to fit residues: 2.3522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 0.0670 chunk 47 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8688 Z= 0.317 Angle : 0.607 6.598 11799 Z= 0.328 Chirality : 0.045 0.149 1345 Planarity : 0.005 0.045 1511 Dihedral : 4.770 26.447 1208 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.29 % Allowed : 16.33 % Favored : 80.38 % 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: 0.15 (0.26), residues: 1095 helix: 1.27 (0.25), residues: 431 sheet: -0.33 (0.35), residues: 222 loop : -0.76 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 298 HIS 0.008 0.002 HIS P 9 PHE 0.023 0.002 PHE A 212 TYR 0.022 0.002 TYR R 297 ARG 0.005 0.001 ARG B 314 *********************** 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 160 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 148 average time/residue: 0.2376 time to fit residues: 46.7303 Evaluate side-chains 141 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1006 time to fit residues: 4.1900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 0.0370 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8688 Z= 0.186 Angle : 0.511 7.945 11799 Z= 0.273 Chirality : 0.042 0.140 1345 Planarity : 0.004 0.045 1511 Dihedral : 4.392 24.495 1208 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.53 % Allowed : 19.15 % Favored : 79.32 % 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: 0.38 (0.26), residues: 1095 helix: 1.60 (0.26), residues: 428 sheet: -0.31 (0.36), residues: 214 loop : -0.71 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 298 HIS 0.005 0.001 HIS A 220 PHE 0.030 0.002 PHE R 315 TYR 0.017 0.001 TYR R 191 ARG 0.004 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 147 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.008 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 144 average time/residue: 0.2429 time to fit residues: 46.8519 Evaluate side-chains 125 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1060 time to fit residues: 1.8441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8688 Z= 0.284 Angle : 0.577 7.750 11799 Z= 0.308 Chirality : 0.044 0.147 1345 Planarity : 0.004 0.047 1511 Dihedral : 4.657 26.106 1208 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.70 % Allowed : 19.74 % Favored : 77.56 % 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: 0.16 (0.25), residues: 1095 helix: 1.38 (0.25), residues: 431 sheet: -0.30 (0.35), residues: 214 loop : -0.90 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.002 PHE R 315 TYR 0.021 0.002 TYR R 297 ARG 0.004 0.001 ARG N 19 *********************** 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 144 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.038 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 0.2600 time to fit residues: 46.6529 Evaluate side-chains 133 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1029 time to fit residues: 4.0844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 B 313 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.4041 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= 0.193 Angle : 0.513 8.410 11799 Z= 0.275 Chirality : 0.041 0.158 1345 Planarity : 0.004 0.046 1511 Dihedral : 4.387 23.983 1208 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.82 % Allowed : 21.50 % Favored : 77.67 % 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: 0.37 (0.26), residues: 1095 helix: 1.69 (0.25), residues: 428 sheet: -0.20 (0.36), residues: 204 loop : -0.90 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 298 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.002 PHE R 335 TYR 0.016 0.001 TYR R 191 ARG 0.003 0.000 ARG B 49 *********************** 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 140 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 139 average time/residue: 0.2523 time to fit residues: 46.5831 Evaluate side-chains 126 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0872 time to fit residues: 1.8479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 96 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 91 HIS B 313 ASN N 31 ASN P 16 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.4241 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= 0.127 Angle : 0.460 6.936 11799 Z= 0.249 Chirality : 0.040 0.132 1345 Planarity : 0.003 0.046 1511 Dihedral : 3.924 17.240 1208 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.94 % Allowed : 22.21 % Favored : 76.85 % 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: 0.70 (0.26), residues: 1095 helix: 2.07 (0.26), residues: 428 sheet: -0.12 (0.36), residues: 196 loop : -0.78 (0.28), residues: 471 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 0.017 0.001 PHE R 335 TYR 0.014 0.001 TYR R 191 ARG 0.006 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 150 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.925 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 145 average time/residue: 0.2581 time to fit residues: 49.0163 Evaluate side-chains 127 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0951 time to fit residues: 2.1197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8688 Z= 0.363 Angle : 0.642 7.471 11799 Z= 0.341 Chirality : 0.046 0.211 1345 Planarity : 0.005 0.048 1511 Dihedral : 4.758 21.427 1208 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.94 % Allowed : 22.91 % Favored : 76.15 % 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: 0.08 (0.25), residues: 1095 helix: 1.42 (0.25), residues: 427 sheet: -0.42 (0.35), residues: 210 loop : -0.99 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.007 0.002 HIS B 266 PHE 0.023 0.002 PHE A 212 TYR 0.012 0.002 TYR A 381 ARG 0.005 0.001 ARG A 273 *********************** 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 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.022 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 138 average time/residue: 0.2641 time to fit residues: 48.3693 Evaluate side-chains 126 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0854 time to fit residues: 2.1756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8688 Z= 0.157 Angle : 0.505 7.483 11799 Z= 0.269 Chirality : 0.041 0.153 1345 Planarity : 0.003 0.048 1511 Dihedral : 4.210 18.835 1208 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.59 % Allowed : 23.15 % 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: 0.46 (0.26), residues: 1095 helix: 1.88 (0.26), residues: 429 sheet: -0.27 (0.35), residues: 206 loop : -0.92 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 298 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.001 PHE R 335 TYR 0.012 0.001 TYR R 191 ARG 0.003 0.000 ARG R 213 ********************** 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 134 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.026 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 131 average time/residue: 0.2510 time to fit residues: 43.7835 Evaluate side-chains 126 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1186 time to fit residues: 1.5130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 36 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN P 16 ASN R 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125459 restraints weight = 12203.033| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.16 r_work: 0.3446 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4385 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 : 0.543 7.627 11799 Z= 0.287 Chirality : 0.042 0.162 1345 Planarity : 0.004 0.048 1511 Dihedral : 4.349 19.939 1208 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.35 % Allowed : 23.50 % Favored : 76.15 % 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: 0.30 (0.26), residues: 1095 helix: 1.72 (0.25), residues: 430 sheet: -0.35 (0.35), residues: 208 loop : -1.00 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.018 0.002 PHE A 212 TYR 0.017 0.001 TYR R 191 ARG 0.003 0.000 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.92 seconds wall clock time: 38 minutes 31.83 seconds (2311.83 seconds total)