Starting phenix.real_space_refine on Sat Jul 20 03:27:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvb_41636/07_2024/8tvb_41636.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvb_41636/07_2024/8tvb_41636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvb_41636/07_2024/8tvb_41636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvb_41636/07_2024/8tvb_41636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvb_41636/07_2024/8tvb_41636.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvb_41636/07_2024/8tvb_41636.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.152 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 60 5.16 5 C 6186 2.51 5 N 1605 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9687 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3173 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3173 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3173 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.66, per 1000 atoms: 0.58 Number of scatterers: 9687 At special positions: 0 Unit cell: (108, 104, 93, 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 60 16.00 O 1836 8.00 N 1605 7.00 C 6186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 288 " distance=2.04 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS A 451 " - pdb=" SG CYS A 459 " distance=2.02 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 488 " distance=2.19 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 513 " distance=2.05 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 451 " - pdb=" SG CYS B 459 " distance=2.02 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 488 " distance=2.19 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 513 " distance=2.05 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 288 " distance=2.04 Simple disulfide: pdb=" SG CYS C 427 " - pdb=" SG CYS C 436 " distance=2.03 Simple disulfide: pdb=" SG CYS C 451 " - pdb=" SG CYS C 459 " distance=2.02 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 488 " distance=2.19 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 513 " distance=2.05 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 195 " " NAG A 902 " - " ASN A 169 " " NAG A 903 " - " ASN A 510 " " NAG A 904 " - " ASN A 160 " " NAG B 901 " - " ASN B 195 " " NAG B 902 " - " ASN B 169 " " NAG B 903 " - " ASN B 510 " " NAG B 904 " - " ASN B 160 " " NAG C 901 " - " ASN C 195 " " NAG C 902 " - " ASN C 169 " " NAG C 903 " - " ASN C 510 " " NAG C 904 " - " ASN C 160 " Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.5 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 37.2% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.878A pdb=" N ILE A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.163A pdb=" N ILE A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.758A pdb=" N GLN A 235 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.668A pdb=" N THR A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.878A pdb=" N ILE B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.163A pdb=" N ILE B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.757A pdb=" N GLN B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 287 through 311 removed outlier: 3.667A pdb=" N THR B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU B 338 " --> pdb=" O ASN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 424 through 427 Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.877A pdb=" N ILE C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 4.162A pdb=" N ILE C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.758A pdb=" N GLN C 235 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 287 through 311 removed outlier: 3.668A pdb=" N THR C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 329 through 332 Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.573A pdb=" N LEU C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 355 Processing helix chain 'C' and resid 424 through 427 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 533 through 537 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429 removed outlier: 7.800A pdb=" N VAL A 434 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU A 141 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS A 436 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS A 143 " --> pdb=" O CYS A 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU A 391 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR A 139 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 389 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU A 141 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA A 387 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS A 143 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N SER A 385 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS A 145 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR A 383 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 411 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 422 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258 removed outlier: 12.690A pdb=" N SER A 150 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 11.608A pdb=" N ASN A 266 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP A 152 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE A 268 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 154 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 371 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE A 365 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 373 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 359 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 322 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.545A pdb=" N LEU C 522 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 220 Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508 Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.708A pdb=" N LEU A 522 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 428 through 429 removed outlier: 7.800A pdb=" N VAL B 434 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU B 141 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS B 436 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS B 143 " --> pdb=" O CYS B 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU B 391 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR B 139 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 389 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU B 141 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA B 387 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS B 143 " --> pdb=" O SER B 385 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N SER B 385 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N LYS B 145 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR B 383 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR B 411 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 422 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 258 removed outlier: 12.691A pdb=" N SER B 150 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N ASN B 266 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP B 152 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE B 268 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 154 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 371 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 365 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 373 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 359 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 322 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB2, first strand: chain 'B' and resid 506 through 508 Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.708A pdb=" N LEU B 522 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 428 through 429 removed outlier: 7.799A pdb=" N VAL C 434 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU C 141 " --> pdb=" O VAL C 434 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N CYS C 436 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 143 " --> pdb=" O CYS C 436 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU C 391 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR C 139 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 389 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU C 141 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA C 387 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N LYS C 143 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N SER C 385 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS C 145 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N THR C 383 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR C 411 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE C 422 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 258 removed outlier: 12.689A pdb=" N SER C 150 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N ASN C 266 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP C 152 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ILE C 268 " --> pdb=" O ASP C 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL C 154 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE C 371 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE C 365 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 373 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 359 " --> pdb=" O TYR C 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 322 " --> pdb=" O GLY C 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 397 through 398 413 hydrogen bonds defined for protein. 1095 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: 3.13 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1948 1.33 - 1.45: 2051 1.45 - 1.58: 5736 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9825 Sorted by residual: bond pdb=" C5 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C5 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C5 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.40e+00 bond pdb=" C5 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" C5 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.413 1.466 -0.053 2.00e-02 2.50e+03 7.10e+00 ... (remaining 9820 not shown) Histogram of bond angle deviations from ideal: 101.32 - 107.80: 246 107.80 - 114.28: 5860 114.28 - 120.76: 4002 120.76 - 127.24: 3221 127.24 - 133.72: 33 Bond angle restraints: 13362 Sorted by residual: angle pdb=" C TYR C 378 " pdb=" N PRO C 379 " pdb=" CA PRO C 379 " ideal model delta sigma weight residual 119.85 127.73 -7.88 1.01e+00 9.80e-01 6.09e+01 angle pdb=" C TYR B 378 " pdb=" N PRO B 379 " pdb=" CA PRO B 379 " ideal model delta sigma weight residual 119.85 127.72 -7.87 1.01e+00 9.80e-01 6.08e+01 angle pdb=" C TYR A 378 " pdb=" N PRO A 379 " pdb=" CA PRO A 379 " ideal model delta sigma weight residual 119.85 127.70 -7.85 1.01e+00 9.80e-01 6.04e+01 angle pdb=" C THR B 147 " pdb=" N PRO B 148 " pdb=" CA PRO B 148 " ideal model delta sigma weight residual 120.31 127.27 -6.96 9.80e-01 1.04e+00 5.05e+01 angle pdb=" C THR C 147 " pdb=" N PRO C 148 " pdb=" CA PRO C 148 " ideal model delta sigma weight residual 120.31 127.25 -6.94 9.80e-01 1.04e+00 5.02e+01 ... (remaining 13357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5934 17.95 - 35.90: 147 35.90 - 53.86: 36 53.86 - 71.81: 21 71.81 - 89.76: 9 Dihedral angle restraints: 6147 sinusoidal: 2442 harmonic: 3705 Sorted by residual: dihedral pdb=" CA PRO B 148 " pdb=" C PRO B 148 " pdb=" N SER B 149 " pdb=" CA SER B 149 " ideal model delta harmonic sigma weight residual 180.00 161.91 18.09 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO A 148 " pdb=" C PRO A 148 " pdb=" N SER A 149 " pdb=" CA SER A 149 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO C 148 " pdb=" C PRO C 148 " pdb=" N SER C 149 " pdb=" CA SER C 149 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1218 0.074 - 0.147: 368 0.147 - 0.221: 67 0.221 - 0.294: 3 0.294 - 0.368: 12 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CA CYS A 288 " pdb=" N CYS A 288 " pdb=" C CYS A 288 " pdb=" CB CYS A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA CYS B 288 " pdb=" N CYS B 288 " pdb=" C CYS B 288 " pdb=" CB CYS B 288 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA CYS C 288 " pdb=" N CYS C 288 " pdb=" C CYS C 288 " pdb=" CB CYS C 288 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1665 not shown) Planarity restraints: 1686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 239 " -0.488 9.50e-02 1.11e+02 2.19e-01 2.93e+01 pdb=" NE ARG C 239 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 239 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 239 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 239 " -0.488 9.50e-02 1.11e+02 2.19e-01 2.93e+01 pdb=" NE ARG B 239 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG B 239 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 239 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 239 " 0.487 9.50e-02 1.11e+02 2.18e-01 2.92e+01 pdb=" NE ARG A 239 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 239 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 239 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 239 " 0.016 2.00e-02 2.50e+03 ... (remaining 1683 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 4682 2.97 - 3.45: 8704 3.45 - 3.93: 15806 3.93 - 4.42: 17854 4.42 - 4.90: 29156 Nonbonded interactions: 76202 Sorted by model distance: nonbonded pdb=" NZ LYS C 151 " pdb=" O LEU C 342 " model vdw 2.487 2.520 nonbonded pdb=" NZ LYS A 151 " pdb=" O LEU A 342 " model vdw 2.487 2.520 nonbonded pdb=" NZ LYS B 151 " pdb=" O LEU B 342 " model vdw 2.487 2.520 nonbonded pdb=" N GLU C 457 " pdb=" OE1 GLU C 457 " model vdw 2.513 2.520 nonbonded pdb=" N GLU A 457 " pdb=" OE1 GLU A 457 " model vdw 2.513 2.520 ... (remaining 76197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.700 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.250 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.055 9825 Z= 0.629 Angle : 1.215 9.035 13362 Z= 0.837 Chirality : 0.075 0.368 1668 Planarity : 0.010 0.219 1674 Dihedral : 10.855 89.758 3720 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.20 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.22), residues: 1254 helix: -1.65 (0.20), residues: 363 sheet: 0.89 (0.32), residues: 252 loop : 0.56 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.004 TRP C 404 HIS 0.005 0.002 HIS C 438 PHE 0.017 0.003 PHE C 371 TYR 0.032 0.003 TYR C 142 ARG 0.005 0.001 ARG C 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7041 (t0) cc_final: 0.6758 (t0) REVERT: A 509 ASP cc_start: 0.7452 (p0) cc_final: 0.7204 (p0) outliers start: 0 outliers final: 1 residues processed: 217 average time/residue: 1.2577 time to fit residues: 291.7629 Evaluate side-chains 132 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.0000 chunk 73 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS B 511 GLN C 482 ASN ** C 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9825 Z= 0.166 Angle : 0.487 5.896 13362 Z= 0.273 Chirality : 0.047 0.188 1668 Planarity : 0.004 0.039 1674 Dihedral : 4.591 29.832 1607 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.39 % Allowed : 8.96 % Favored : 89.65 % 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: 0.65 (0.23), residues: 1254 helix: 0.12 (0.26), residues: 390 sheet: 1.12 (0.29), residues: 297 loop : 0.47 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 404 HIS 0.005 0.001 HIS C 438 PHE 0.013 0.002 PHE B 371 TYR 0.016 0.001 TYR A 468 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.191 Fit side-chains REVERT: A 372 MET cc_start: 0.8599 (mtm) cc_final: 0.8335 (mtm) REVERT: A 514 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7430 (t) REVERT: B 520 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: C 166 LYS cc_start: 0.6779 (mmmm) cc_final: 0.6485 (tttp) REVERT: C 334 ASN cc_start: 0.7853 (t0) cc_final: 0.7520 (t0) outliers start: 14 outliers final: 3 residues processed: 153 average time/residue: 1.2048 time to fit residues: 197.7580 Evaluate side-chains 118 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 538 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 113 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN B 334 ASN B 511 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9825 Z= 0.159 Angle : 0.456 5.512 13362 Z= 0.252 Chirality : 0.046 0.154 1668 Planarity : 0.004 0.036 1674 Dihedral : 4.047 24.546 1605 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.67 % Favored : 98.09 % Rotamer: Outliers : 1.49 % Allowed : 11.04 % Favored : 87.46 % 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: 0.90 (0.24), residues: 1254 helix: 0.86 (0.27), residues: 393 sheet: 0.84 (0.30), residues: 279 loop : 0.47 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 404 HIS 0.004 0.001 HIS C 438 PHE 0.015 0.002 PHE A 310 TYR 0.028 0.001 TYR A 468 ARG 0.009 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.122 Fit side-chains REVERT: A 245 ASP cc_start: 0.7306 (m-30) cc_final: 0.7080 (m-30) REVERT: C 520 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6718 (mp0) outliers start: 15 outliers final: 1 residues processed: 143 average time/residue: 1.1060 time to fit residues: 170.5798 Evaluate side-chains 107 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 272 GLN B 334 ASN B 511 GLN C 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9825 Z= 0.215 Angle : 0.475 5.422 13362 Z= 0.257 Chirality : 0.047 0.151 1668 Planarity : 0.004 0.039 1674 Dihedral : 4.075 20.115 1605 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.59 % Favored : 98.17 % Rotamer: Outliers : 1.59 % Allowed : 12.04 % Favored : 86.37 % 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: 0.84 (0.24), residues: 1254 helix: 0.90 (0.28), residues: 390 sheet: 0.77 (0.30), residues: 261 loop : 0.38 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 404 HIS 0.004 0.001 HIS C 438 PHE 0.017 0.002 PHE C 371 TYR 0.017 0.001 TYR A 468 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.706 Fit side-chains REVERT: A 243 LEU cc_start: 0.8299 (mt) cc_final: 0.8036 (mt) REVERT: B 520 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6349 (mp0) outliers start: 16 outliers final: 7 residues processed: 130 average time/residue: 1.2656 time to fit residues: 177.0344 Evaluate side-chains 112 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 405 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 347 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9825 Z= 0.173 Angle : 0.435 4.771 13362 Z= 0.238 Chirality : 0.046 0.144 1668 Planarity : 0.004 0.039 1674 Dihedral : 3.867 19.690 1605 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.83 % Favored : 97.93 % Rotamer: Outliers : 1.09 % Allowed : 13.53 % Favored : 85.37 % 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: 0.87 (0.24), residues: 1254 helix: 1.12 (0.28), residues: 390 sheet: 0.72 (0.31), residues: 261 loop : 0.29 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 404 HIS 0.003 0.001 HIS C 438 PHE 0.013 0.001 PHE C 371 TYR 0.015 0.001 TYR A 468 ARG 0.002 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.171 Fit side-chains REVERT: B 520 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: C 520 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6677 (mp0) outliers start: 11 outliers final: 4 residues processed: 114 average time/residue: 1.2697 time to fit residues: 155.7553 Evaluate side-chains 104 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 538 HIS Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.3980 chunk 109 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 0.0030 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN C 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9825 Z= 0.124 Angle : 0.407 4.587 13362 Z= 0.224 Chirality : 0.046 0.188 1668 Planarity : 0.003 0.041 1674 Dihedral : 3.736 23.519 1605 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.36 % Favored : 98.41 % Rotamer: Outliers : 0.90 % Allowed : 13.93 % Favored : 85.17 % 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: 0.81 (0.24), residues: 1254 helix: 1.34 (0.28), residues: 393 sheet: 0.53 (0.30), residues: 285 loop : 0.09 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 404 HIS 0.003 0.001 HIS C 438 PHE 0.010 0.001 PHE C 371 TYR 0.016 0.001 TYR B 468 ARG 0.005 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.026 Fit side-chains REVERT: B 520 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: C 198 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7494 (ptpp) REVERT: C 520 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6652 (mp0) outliers start: 9 outliers final: 3 residues processed: 117 average time/residue: 1.2514 time to fit residues: 156.8134 Evaluate side-chains 108 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 HIS Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 520 GLU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 520 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 68 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 0.0970 chunk 76 optimal weight: 0.0170 chunk 74 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 347 ASN B 511 GLN C 398 ASN ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.022 9825 Z= 0.101 Angle : 0.389 4.499 13362 Z= 0.215 Chirality : 0.045 0.147 1668 Planarity : 0.003 0.041 1674 Dihedral : 3.521 22.437 1605 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.12 % Favored : 98.64 % Rotamer: Outliers : 0.60 % Allowed : 15.42 % Favored : 83.98 % 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: 1.05 (0.24), residues: 1254 helix: 1.65 (0.28), residues: 396 sheet: 0.67 (0.30), residues: 285 loop : 0.13 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 404 HIS 0.003 0.000 HIS C 438 PHE 0.010 0.001 PHE C 331 TYR 0.016 0.001 TYR A 446 ARG 0.008 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.135 Fit side-chains REVERT: C 198 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7922 (pttp) outliers start: 6 outliers final: 0 residues processed: 128 average time/residue: 1.2042 time to fit residues: 165.6635 Evaluate side-chains 111 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 347 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 347 ASN B 511 GLN C 398 ASN C 511 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9825 Z= 0.202 Angle : 0.461 6.054 13362 Z= 0.246 Chirality : 0.047 0.144 1668 Planarity : 0.003 0.041 1674 Dihedral : 3.826 21.508 1605 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.59 % Favored : 98.17 % Rotamer: Outliers : 0.60 % Allowed : 15.52 % Favored : 83.88 % 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: 0.95 (0.24), residues: 1254 helix: 1.45 (0.28), residues: 393 sheet: 0.75 (0.31), residues: 261 loop : 0.13 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 404 HIS 0.003 0.001 HIS C 438 PHE 0.016 0.002 PHE C 371 TYR 0.017 0.001 TYR B 468 ARG 0.004 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.179 Fit side-chains REVERT: A 537 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6497 (pp-130) outliers start: 6 outliers final: 2 residues processed: 119 average time/residue: 1.1285 time to fit residues: 145.1517 Evaluate side-chains 105 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 538 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 347 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9825 Z= 0.170 Angle : 0.443 6.412 13362 Z= 0.237 Chirality : 0.047 0.142 1668 Planarity : 0.003 0.040 1674 Dihedral : 3.839 20.346 1605 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.36 % Favored : 98.41 % Rotamer: Outliers : 0.60 % Allowed : 16.32 % Favored : 83.08 % 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: 0.86 (0.24), residues: 1254 helix: 1.44 (0.28), residues: 393 sheet: 0.65 (0.31), residues: 261 loop : 0.04 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 404 HIS 0.003 0.001 HIS C 438 PHE 0.013 0.001 PHE C 371 TYR 0.018 0.001 TYR B 446 ARG 0.005 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.087 Fit side-chains REVERT: A 537 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6288 (pp-130) REVERT: C 198 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7445 (ptpp) outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 1.1799 time to fit residues: 141.1797 Evaluate side-chains 109 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain C residue 198 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0030 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 398 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 511 GLN C 532 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9825 Z= 0.157 Angle : 0.455 7.328 13362 Z= 0.241 Chirality : 0.046 0.141 1668 Planarity : 0.003 0.040 1674 Dihedral : 3.864 21.306 1605 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.52 % Favored : 98.25 % Rotamer: Outliers : 0.50 % Allowed : 16.52 % Favored : 82.99 % 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: 0.84 (0.24), residues: 1254 helix: 1.42 (0.28), residues: 396 sheet: 0.66 (0.31), residues: 261 loop : 0.02 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 404 HIS 0.003 0.001 HIS C 438 PHE 0.012 0.001 PHE C 371 TYR 0.015 0.001 TYR B 468 ARG 0.006 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.167 Fit side-chains REVERT: A 537 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6285 (pp-130) outliers start: 5 outliers final: 3 residues processed: 108 average time/residue: 1.1294 time to fit residues: 132.3589 Evaluate side-chains 102 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 506 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 511 GLN C 511 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112298 restraints weight = 11195.310| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.93 r_work: 0.3135 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9825 Z= 0.345 Angle : 0.576 8.786 13362 Z= 0.299 Chirality : 0.050 0.151 1668 Planarity : 0.004 0.039 1674 Dihedral : 4.496 23.249 1605 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.99 % Favored : 97.85 % Rotamer: Outliers : 0.40 % Allowed : 16.82 % Favored : 82.79 % 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 (0.23), residues: 1254 helix: 0.88 (0.27), residues: 390 sheet: 0.53 (0.31), residues: 258 loop : -0.06 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 404 HIS 0.004 0.001 HIS C 438 PHE 0.022 0.002 PHE C 371 TYR 0.020 0.002 TYR B 446 ARG 0.005 0.001 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.80 seconds wall clock time: 59 minutes 58.02 seconds (3598.02 seconds total)