Starting phenix.real_space_refine on Wed Feb 14 16:01:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/02_2024/6ave_7009.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/02_2024/6ave_7009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/02_2024/6ave_7009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/02_2024/6ave_7009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/02_2024/6ave_7009.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/02_2024/6ave_7009.pdb" } resolution = 3.7 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= 0.031 sd= 1.102 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 81 5.16 5 C 6204 2.51 5 N 1581 2.21 5 O 1791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9657 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3191 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 403} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3191 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 403} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3191 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 403} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.45, per 1000 atoms: 0.67 Number of scatterers: 9657 At special positions: 0 Unit cell: (95.68, 98.8, 128.96, 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 81 16.00 O 1791 8.00 N 1581 7.00 C 6204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 195 " distance=2.01 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 195 " distance=2.01 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 366 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 195 " distance=2.01 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 366 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 362 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 336 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 394 " " NAG A 602 " - " ASN A 367 " " NAG B 601 " - " ASN B 394 " " NAG B 602 " - " ASN B 367 " " NAG C 601 " - " ASN C 394 " " NAG C 602 " - " ASN C 367 " Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 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: 45 helices and 12 sheets defined 40.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 41 through 70 Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 132 through 143 removed outlier: 3.712A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.733A pdb=" N PHE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.522A pdb=" N TYR A 230 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.895A pdb=" N ASN A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.728A pdb=" N LYS A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.814A pdb=" N CYS A 360 " --> pdb=" O ASN A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 394 removed outlier: 3.722A pdb=" N LEU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 426 through 441 Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.821A pdb=" N LYS A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N HIS A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 70 Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 132 through 143 removed outlier: 3.712A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.734A pdb=" N PHE B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.521A pdb=" N TYR B 230 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.895A pdb=" N ASN B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.726A pdb=" N LYS B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.815A pdb=" N CYS B 360 " --> pdb=" O ASN B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 394 removed outlier: 3.721A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 426 through 441 Processing helix chain 'B' and resid 445 through 464 removed outlier: 3.822A pdb=" N LYS B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 70 Processing helix chain 'C' and resid 105 through 113 Processing helix chain 'C' and resid 132 through 143 removed outlier: 3.711A pdb=" N LEU C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.734A pdb=" N PHE C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.522A pdb=" N TYR C 230 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.896A pdb=" N ASN C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 344 removed outlier: 3.727A pdb=" N LYS C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.814A pdb=" N CYS C 360 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 394 removed outlier: 3.722A pdb=" N LEU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 445 through 464 removed outlier: 3.822A pdb=" N LYS C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN A 415 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU A 278 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 270 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 172 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP A 224 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A 170 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN A 415 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU A 278 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.670A pdb=" N LEU A 86 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189 removed outlier: 7.102A pdb=" N LYS A 194 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASN A 95 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN B 415 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU B 278 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B 270 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 172 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP B 224 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 170 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN B 415 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU B 278 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.670A pdb=" N LEU B 86 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 185 through 189 removed outlier: 7.102A pdb=" N LYS B 194 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN B 95 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN C 415 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C 278 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C 270 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER C 172 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP C 224 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 170 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 82 removed outlier: 7.397A pdb=" N ASN C 415 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C 278 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.670A pdb=" N LEU C 86 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 185 through 189 removed outlier: 7.102A pdb=" N LYS C 194 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN C 95 " --> pdb=" O LYS C 194 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1515 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: 2.81 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3120 1.35 - 1.47: 2594 1.47 - 1.60: 4063 1.60 - 1.73: 0 1.73 - 1.85: 111 Bond restraints: 9888 Sorted by residual: bond pdb=" CG1 ILE C 259 " pdb=" CD1 ILE C 259 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CG1 ILE A 259 " pdb=" CD1 ILE A 259 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.68e+00 bond pdb=" CG1 ILE B 259 " pdb=" CD1 ILE B 259 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.66e+00 bond pdb=" C ASN C 367 " pdb=" N VAL C 368 " ideal model delta sigma weight residual 1.329 1.286 0.044 2.19e-02 2.09e+03 3.97e+00 bond pdb=" C ASN A 367 " pdb=" N VAL A 368 " ideal model delta sigma weight residual 1.329 1.287 0.043 2.19e-02 2.09e+03 3.78e+00 ... (remaining 9883 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.80: 318 106.80 - 113.91: 5512 113.91 - 121.02: 4917 121.02 - 128.13: 2649 128.13 - 135.24: 62 Bond angle restraints: 13458 Sorted by residual: angle pdb=" C ILE B 380 " pdb=" N PRO B 381 " pdb=" CA PRO B 381 " ideal model delta sigma weight residual 127.00 135.24 -8.24 2.40e+00 1.74e-01 1.18e+01 angle pdb=" C ILE C 380 " pdb=" N PRO C 381 " pdb=" CA PRO C 381 " ideal model delta sigma weight residual 127.00 135.24 -8.24 2.40e+00 1.74e-01 1.18e+01 angle pdb=" C ILE A 380 " pdb=" N PRO A 381 " pdb=" CA PRO A 381 " ideal model delta sigma weight residual 127.00 135.21 -8.21 2.40e+00 1.74e-01 1.17e+01 angle pdb=" C ILE C 380 " pdb=" N PRO C 381 " pdb=" CD PRO C 381 " ideal model delta sigma weight residual 120.60 113.64 6.96 2.20e+00 2.07e-01 1.00e+01 angle pdb=" C ILE B 380 " pdb=" N PRO B 381 " pdb=" CD PRO B 381 " ideal model delta sigma weight residual 120.60 113.64 6.96 2.20e+00 2.07e-01 1.00e+01 ... (remaining 13453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 5680 15.16 - 30.32: 236 30.32 - 45.48: 45 45.48 - 60.64: 18 60.64 - 75.80: 6 Dihedral angle restraints: 5985 sinusoidal: 2268 harmonic: 3717 Sorted by residual: dihedral pdb=" CA THR B 337 " pdb=" C THR B 337 " pdb=" N PRO B 338 " pdb=" CA PRO B 338 " ideal model delta harmonic sigma weight residual 180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA THR C 337 " pdb=" C THR C 337 " pdb=" N PRO C 338 " pdb=" CA PRO C 338 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA THR A 337 " pdb=" C THR A 337 " pdb=" N PRO A 338 " pdb=" CA PRO A 338 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 5982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 1500 0.189 - 0.378: 9 0.378 - 0.567: 0 0.567 - 0.756: 0 0.756 - 0.945: 3 Chirality restraints: 1512 Sorted by residual: chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 367 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 367 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 367 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 1509 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 107 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ASN C 107 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN C 107 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 108 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 107 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ASN B 107 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 107 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP B 108 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 107 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C ASN A 107 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN A 107 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 108 " -0.013 2.00e-02 2.50e+03 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3161 2.82 - 3.34: 8653 3.34 - 3.86: 15709 3.86 - 4.38: 18193 4.38 - 4.90: 30272 Nonbonded interactions: 75988 Sorted by model distance: nonbonded pdb=" OG1 THR C 215 " pdb=" OD2 ASP C 408 " model vdw 2.301 2.440 nonbonded pdb=" OG1 THR B 215 " pdb=" OD2 ASP B 408 " model vdw 2.302 2.440 nonbonded pdb=" OG1 THR A 215 " pdb=" OD2 ASP A 408 " model vdw 2.302 2.440 nonbonded pdb=" NE2 HIS B 111 " pdb=" O LYS B 151 " model vdw 2.308 2.520 nonbonded pdb=" NE2 HIS C 111 " pdb=" O LYS C 151 " model vdw 2.308 2.520 ... (remaining 75983 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 2.190 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.720 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 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 : 0.008 0.085 9888 Z= 0.518 Angle : 0.878 9.296 13458 Z= 0.474 Chirality : 0.068 0.945 1512 Planarity : 0.005 0.040 1749 Dihedral : 9.624 75.799 3540 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.23 (0.20), residues: 1266 helix: -2.76 (0.17), residues: 432 sheet: -1.68 (0.28), residues: 279 loop : -1.67 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 47 HIS 0.010 0.002 HIS C 251 PHE 0.023 0.003 PHE B 453 TYR 0.030 0.003 TYR C 393 ARG 0.008 0.001 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8838 (t80) cc_final: 0.8329 (t80) REVERT: A 198 PHE cc_start: 0.8663 (t80) cc_final: 0.8453 (t80) REVERT: A 217 ASN cc_start: 0.7848 (m110) cc_final: 0.6891 (t0) REVERT: A 247 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8240 (ttmm) REVERT: A 249 GLN cc_start: 0.7706 (tm-30) cc_final: 0.6784 (tm-30) REVERT: A 278 GLU cc_start: 0.8390 (tt0) cc_final: 0.7708 (tt0) REVERT: A 309 CYS cc_start: 0.6570 (t) cc_final: 0.6331 (t) REVERT: A 323 ASN cc_start: 0.8097 (m-40) cc_final: 0.7864 (m110) REVERT: A 341 TYR cc_start: 0.7407 (m-10) cc_final: 0.7178 (m-10) REVERT: A 350 ASP cc_start: 0.8450 (m-30) cc_final: 0.8023 (m-30) REVERT: A 379 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7976 (tptt) REVERT: A 420 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 454 ASP cc_start: 0.8266 (m-30) cc_final: 0.7878 (m-30) REVERT: B 217 ASN cc_start: 0.7801 (m110) cc_final: 0.6800 (t0) REVERT: B 249 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7520 (tt0) REVERT: B 262 LEU cc_start: 0.9124 (mt) cc_final: 0.8839 (mp) REVERT: B 278 GLU cc_start: 0.8303 (tt0) cc_final: 0.7838 (tt0) REVERT: B 280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8114 (mtt180) REVERT: B 309 CYS cc_start: 0.6657 (t) cc_final: 0.6456 (t) REVERT: B 350 ASP cc_start: 0.8312 (m-30) cc_final: 0.7897 (m-30) REVERT: B 420 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 61 VAL cc_start: 0.8623 (m) cc_final: 0.8221 (p) REVERT: C 220 GLU cc_start: 0.7506 (tt0) cc_final: 0.7157 (tt0) REVERT: C 247 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8088 (ttmm) REVERT: C 278 GLU cc_start: 0.8318 (tt0) cc_final: 0.7666 (tt0) REVERT: C 280 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7560 (mtt180) REVERT: C 309 CYS cc_start: 0.6709 (t) cc_final: 0.6445 (t) REVERT: C 341 TYR cc_start: 0.7366 (m-10) cc_final: 0.7072 (m-10) REVERT: C 350 ASP cc_start: 0.8432 (m-30) cc_final: 0.8061 (m-30) REVERT: C 373 LYS cc_start: 0.7872 (pttm) cc_final: 0.7580 (mttt) REVERT: C 379 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7749 (tptp) REVERT: C 403 ASN cc_start: 0.8128 (m-40) cc_final: 0.7447 (m110) REVERT: C 420 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7335 (mt-10) REVERT: C 437 GLN cc_start: 0.8921 (mt0) cc_final: 0.8575 (mt0) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.2543 time to fit residues: 144.4753 Evaluate side-chains 246 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 403 ASN C 249 GLN C 277 GLN ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9888 Z= 0.260 Angle : 0.667 7.748 13458 Z= 0.350 Chirality : 0.047 0.456 1512 Planarity : 0.004 0.034 1749 Dihedral : 6.392 40.823 1500 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.32 % Allowed : 15.43 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.55 (0.23), residues: 1266 helix: -0.66 (0.23), residues: 441 sheet: -1.46 (0.29), residues: 291 loop : -0.88 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 47 HIS 0.007 0.002 HIS A 111 PHE 0.023 0.002 PHE B 270 TYR 0.016 0.002 TYR C 230 ARG 0.009 0.001 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 281 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8905 (t80) cc_final: 0.8177 (t80) REVERT: A 108 ASP cc_start: 0.7223 (m-30) cc_final: 0.6914 (m-30) REVERT: A 217 ASN cc_start: 0.7917 (m110) cc_final: 0.6843 (t0) REVERT: A 220 GLU cc_start: 0.7643 (tt0) cc_final: 0.7241 (mt-10) REVERT: A 242 PHE cc_start: 0.8857 (m-80) cc_final: 0.8648 (m-80) REVERT: A 249 GLN cc_start: 0.7963 (tm-30) cc_final: 0.6980 (tm-30) REVERT: A 280 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7566 (mtt180) REVERT: A 309 CYS cc_start: 0.6867 (t) cc_final: 0.6551 (t) REVERT: A 326 MET cc_start: 0.7550 (mmt) cc_final: 0.7194 (mmm) REVERT: A 379 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7817 (tptt) REVERT: A 402 GLU cc_start: 0.8062 (pt0) cc_final: 0.7634 (pp20) REVERT: A 430 LEU cc_start: 0.9015 (tp) cc_final: 0.8804 (tt) REVERT: B 217 ASN cc_start: 0.7763 (m110) cc_final: 0.6739 (t0) REVERT: B 249 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 278 GLU cc_start: 0.8224 (tt0) cc_final: 0.7775 (tt0) REVERT: B 309 CYS cc_start: 0.6812 (t) cc_final: 0.6541 (t) REVERT: B 326 MET cc_start: 0.7678 (mmt) cc_final: 0.7338 (mmt) REVERT: B 420 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7354 (mt-10) REVERT: C 87 THR cc_start: 0.9188 (m) cc_final: 0.8845 (t) REVERT: C 108 ASP cc_start: 0.7204 (m-30) cc_final: 0.6879 (m-30) REVERT: C 155 MET cc_start: 0.8282 (mmm) cc_final: 0.7981 (tpt) REVERT: C 258 LEU cc_start: 0.8177 (tp) cc_final: 0.7962 (tp) REVERT: C 278 GLU cc_start: 0.8326 (tt0) cc_final: 0.7784 (tt0) REVERT: C 280 ARG cc_start: 0.8452 (mtt180) cc_final: 0.8017 (mtt180) REVERT: C 309 CYS cc_start: 0.6890 (t) cc_final: 0.6620 (t) REVERT: C 379 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7724 (tptp) REVERT: C 403 ASN cc_start: 0.8313 (m-40) cc_final: 0.7604 (m110) outliers start: 31 outliers final: 15 residues processed: 296 average time/residue: 0.1864 time to fit residues: 79.0352 Evaluate side-chains 257 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 242 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 396 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 9888 Z= 0.539 Angle : 0.781 7.900 13458 Z= 0.415 Chirality : 0.050 0.383 1512 Planarity : 0.005 0.031 1749 Dihedral : 6.169 29.735 1500 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.36 % Allowed : 18.44 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.22 (0.24), residues: 1266 helix: -0.17 (0.25), residues: 441 sheet: -1.76 (0.29), residues: 267 loop : -0.65 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 234 HIS 0.009 0.002 HIS B 111 PHE 0.021 0.003 PHE B 93 TYR 0.025 0.003 TYR C 110 ARG 0.010 0.001 ARG C 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 250 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.7539 (m-30) cc_final: 0.7102 (m-30) REVERT: A 220 GLU cc_start: 0.7746 (tt0) cc_final: 0.7188 (mt-10) REVERT: A 249 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 326 MET cc_start: 0.7700 (mmm) cc_final: 0.7179 (mmm) REVERT: A 379 LYS cc_start: 0.8619 (ttpt) cc_final: 0.7972 (tptt) REVERT: B 220 GLU cc_start: 0.7672 (tt0) cc_final: 0.7180 (mt-10) REVERT: B 222 MET cc_start: 0.8666 (ttp) cc_final: 0.8257 (ttm) REVERT: B 249 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7358 (tm-30) REVERT: B 275 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.7910 (p) REVERT: B 280 ARG cc_start: 0.8463 (mtt180) cc_final: 0.7859 (mtt180) REVERT: B 309 CYS cc_start: 0.6901 (t) cc_final: 0.6668 (t) REVERT: B 420 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7515 (mt-10) REVERT: C 60 LEU cc_start: 0.8660 (tp) cc_final: 0.8441 (tt) REVERT: C 275 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.7777 (p) REVERT: C 280 ARG cc_start: 0.8428 (mtt180) cc_final: 0.7913 (mtt180) REVERT: C 309 CYS cc_start: 0.6970 (t) cc_final: 0.6700 (t) REVERT: C 379 LYS cc_start: 0.8464 (ttpt) cc_final: 0.7766 (tptp) outliers start: 50 outliers final: 28 residues processed: 276 average time/residue: 0.2255 time to fit residues: 89.2001 Evaluate side-chains 238 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 0.0980 chunk 32 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9888 Z= 0.191 Angle : 0.597 6.921 13458 Z= 0.311 Chirality : 0.044 0.346 1512 Planarity : 0.004 0.033 1749 Dihedral : 5.427 25.478 1500 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.11 % Allowed : 22.94 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.56 (0.25), residues: 1266 helix: 0.59 (0.25), residues: 441 sheet: -1.41 (0.30), residues: 297 loop : -0.37 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS A 111 PHE 0.017 0.001 PHE A 270 TYR 0.018 0.001 TYR C 68 ARG 0.004 0.000 ARG C 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.7004 (m-30) cc_final: 0.6734 (m-30) REVERT: A 171 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 220 GLU cc_start: 0.7568 (tt0) cc_final: 0.7054 (mt-10) REVERT: A 249 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 326 MET cc_start: 0.7677 (mmt) cc_final: 0.7136 (mmm) REVERT: A 379 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7753 (tptt) REVERT: B 60 LEU cc_start: 0.8455 (tp) cc_final: 0.8223 (tt) REVERT: B 220 GLU cc_start: 0.7548 (tt0) cc_final: 0.7061 (mt-10) REVERT: B 222 MET cc_start: 0.8590 (ttp) cc_final: 0.8373 (ttm) REVERT: B 249 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7356 (tm-30) REVERT: B 314 GLU cc_start: 0.7329 (mp0) cc_final: 0.7012 (mp0) REVERT: B 326 MET cc_start: 0.7680 (mmt) cc_final: 0.7473 (mmt) REVERT: B 420 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 309 CYS cc_start: 0.6797 (t) cc_final: 0.6557 (t) REVERT: C 379 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7590 (tptp) outliers start: 29 outliers final: 20 residues processed: 252 average time/residue: 0.1958 time to fit residues: 71.2562 Evaluate side-chains 232 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.0670 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.0370 chunk 109 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9888 Z= 0.159 Angle : 0.553 8.355 13458 Z= 0.287 Chirality : 0.043 0.337 1512 Planarity : 0.003 0.030 1749 Dihedral : 4.830 23.011 1500 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.86 % Allowed : 22.83 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1266 helix: 1.10 (0.26), residues: 438 sheet: -1.26 (0.30), residues: 297 loop : -0.21 (0.31), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 47 HIS 0.003 0.001 HIS B 111 PHE 0.013 0.001 PHE B 270 TYR 0.016 0.001 TYR C 68 ARG 0.004 0.001 ARG C 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 222 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8437 (tp) cc_final: 0.8218 (tt) REVERT: A 97 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7191 (t0) REVERT: A 220 GLU cc_start: 0.7580 (tt0) cc_final: 0.7124 (mt-10) REVERT: A 249 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 326 MET cc_start: 0.7647 (mmt) cc_final: 0.7096 (mmm) REVERT: A 379 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7725 (tptt) REVERT: A 422 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8572 (mmtm) REVERT: A 425 TYR cc_start: 0.8576 (t80) cc_final: 0.6928 (t80) REVERT: B 220 GLU cc_start: 0.7518 (tt0) cc_final: 0.6953 (mt-10) REVERT: B 222 MET cc_start: 0.8560 (ttp) cc_final: 0.8287 (ttm) REVERT: B 249 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7287 (tt0) REVERT: B 262 LEU cc_start: 0.9190 (mp) cc_final: 0.8766 (mp) REVERT: B 275 SER cc_start: 0.8900 (m) cc_final: 0.7908 (p) REVERT: B 314 GLU cc_start: 0.7368 (mp0) cc_final: 0.7028 (mp0) REVERT: B 326 MET cc_start: 0.7750 (mmt) cc_final: 0.7534 (mmt) REVERT: B 405 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8684 (pp) REVERT: B 420 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 280 ARG cc_start: 0.8593 (mtt180) cc_final: 0.7700 (mtt180) REVERT: C 326 MET cc_start: 0.7877 (mmt) cc_final: 0.7581 (mmt) REVERT: C 379 LYS cc_start: 0.8264 (ttpt) cc_final: 0.7504 (tptp) outliers start: 36 outliers final: 28 residues processed: 245 average time/residue: 0.1934 time to fit residues: 67.9621 Evaluate side-chains 237 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 207 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9888 Z= 0.222 Angle : 0.579 7.943 13458 Z= 0.295 Chirality : 0.043 0.330 1512 Planarity : 0.003 0.029 1749 Dihedral : 4.696 22.423 1500 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.86 % Allowed : 23.26 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.01 (0.25), residues: 1266 helix: 1.28 (0.26), residues: 438 sheet: -1.20 (0.30), residues: 297 loop : -0.17 (0.30), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.004 0.001 HIS B 111 PHE 0.011 0.001 PHE A 270 TYR 0.015 0.001 TYR C 68 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 1.113 Fit side-chains REVERT: A 220 GLU cc_start: 0.7567 (tt0) cc_final: 0.7056 (mt-10) REVERT: A 224 ASP cc_start: 0.8572 (t0) cc_final: 0.8308 (t0) REVERT: A 249 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 280 ARG cc_start: 0.8501 (mtt180) cc_final: 0.7382 (mtt180) REVERT: A 326 MET cc_start: 0.7695 (mmt) cc_final: 0.7123 (mmm) REVERT: A 379 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7772 (tptt) REVERT: A 425 TYR cc_start: 0.8563 (t80) cc_final: 0.6908 (t80) REVERT: B 220 GLU cc_start: 0.7521 (tt0) cc_final: 0.6979 (mt-10) REVERT: B 222 MET cc_start: 0.8564 (ttp) cc_final: 0.8278 (ttm) REVERT: B 249 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7243 (tt0) REVERT: B 262 LEU cc_start: 0.9202 (mp) cc_final: 0.8752 (mp) REVERT: B 275 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.7927 (p) REVERT: B 314 GLU cc_start: 0.7384 (mp0) cc_final: 0.7028 (mp0) REVERT: B 326 MET cc_start: 0.7742 (mmt) cc_final: 0.7476 (mmt) REVERT: B 405 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8717 (pp) REVERT: B 420 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 275 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.7947 (p) REVERT: C 326 MET cc_start: 0.7938 (mmt) cc_final: 0.7589 (mmt) REVERT: C 379 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7569 (tptp) outliers start: 36 outliers final: 27 residues processed: 235 average time/residue: 0.1867 time to fit residues: 63.5830 Evaluate side-chains 241 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 417 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 74 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9888 Z= 0.205 Angle : 0.586 9.821 13458 Z= 0.294 Chirality : 0.043 0.324 1512 Planarity : 0.003 0.028 1749 Dihedral : 4.586 21.584 1500 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.39 % Allowed : 22.08 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.26), residues: 1266 helix: 1.26 (0.26), residues: 444 sheet: -1.23 (0.30), residues: 300 loop : -0.03 (0.31), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 47 HIS 0.004 0.001 HIS B 111 PHE 0.011 0.001 PHE B 270 TYR 0.013 0.001 TYR C 68 ARG 0.003 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 1.068 Fit side-chains REVERT: A 220 GLU cc_start: 0.7520 (tt0) cc_final: 0.7108 (mt-10) REVERT: A 224 ASP cc_start: 0.8572 (t0) cc_final: 0.8272 (t0) REVERT: A 249 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 280 ARG cc_start: 0.8508 (mtt180) cc_final: 0.7435 (mtt180) REVERT: A 326 MET cc_start: 0.7706 (mmt) cc_final: 0.7106 (mmm) REVERT: A 379 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7760 (tptt) REVERT: B 220 GLU cc_start: 0.7482 (tt0) cc_final: 0.6958 (mt-10) REVERT: B 222 MET cc_start: 0.8563 (ttp) cc_final: 0.8292 (ttm) REVERT: B 249 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7231 (tt0) REVERT: B 262 LEU cc_start: 0.9201 (mp) cc_final: 0.8741 (mp) REVERT: B 275 SER cc_start: 0.8869 (m) cc_final: 0.7953 (p) REVERT: B 314 GLU cc_start: 0.7391 (mp0) cc_final: 0.7037 (mp0) REVERT: B 326 MET cc_start: 0.7722 (mmt) cc_final: 0.7419 (mmt) REVERT: B 405 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8708 (pp) REVERT: B 420 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 275 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.7999 (p) REVERT: C 326 MET cc_start: 0.7873 (mmt) cc_final: 0.7522 (mmt) REVERT: C 379 LYS cc_start: 0.8387 (ttpt) cc_final: 0.7616 (tptp) REVERT: C 437 GLN cc_start: 0.8487 (mt0) cc_final: 0.8191 (mt0) outliers start: 41 outliers final: 35 residues processed: 247 average time/residue: 0.1755 time to fit residues: 63.6350 Evaluate side-chains 249 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 445 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9888 Z= 0.176 Angle : 0.558 7.753 13458 Z= 0.283 Chirality : 0.043 0.321 1512 Planarity : 0.003 0.036 1749 Dihedral : 4.442 20.810 1500 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.50 % Allowed : 21.86 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.21 (0.26), residues: 1266 helix: 1.33 (0.26), residues: 444 sheet: -1.09 (0.30), residues: 297 loop : 0.04 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 47 HIS 0.003 0.001 HIS B 111 PHE 0.010 0.001 PHE B 270 TYR 0.011 0.001 TYR C 68 ARG 0.003 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 1.065 Fit side-chains REVERT: A 220 GLU cc_start: 0.7461 (tt0) cc_final: 0.7026 (mt-10) REVERT: A 249 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 280 ARG cc_start: 0.8523 (mtt180) cc_final: 0.7458 (mtt180) REVERT: A 326 MET cc_start: 0.7724 (mmt) cc_final: 0.7159 (mmm) REVERT: A 379 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8150 (tttp) REVERT: A 422 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8602 (mmmm) REVERT: A 425 TYR cc_start: 0.8493 (t80) cc_final: 0.6991 (t80) REVERT: B 220 GLU cc_start: 0.7441 (tt0) cc_final: 0.6915 (mt-10) REVERT: B 249 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7265 (tt0) REVERT: B 262 LEU cc_start: 0.9204 (mp) cc_final: 0.8779 (mp) REVERT: B 275 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.7970 (p) REVERT: B 314 GLU cc_start: 0.7443 (mp0) cc_final: 0.7087 (mp0) REVERT: B 326 MET cc_start: 0.7682 (mmt) cc_final: 0.7356 (mmt) REVERT: B 405 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8674 (pp) REVERT: B 420 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7592 (mt-10) REVERT: C 275 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8021 (p) REVERT: C 326 MET cc_start: 0.7840 (mmt) cc_final: 0.7481 (mmt) REVERT: C 379 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7627 (tptt) outliers start: 42 outliers final: 37 residues processed: 245 average time/residue: 0.1769 time to fit residues: 63.5078 Evaluate side-chains 252 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 445 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9888 Z= 0.218 Angle : 0.586 8.083 13458 Z= 0.295 Chirality : 0.043 0.317 1512 Planarity : 0.004 0.037 1749 Dihedral : 4.480 21.095 1500 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.39 % Allowed : 22.29 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.19 (0.26), residues: 1266 helix: 1.33 (0.26), residues: 444 sheet: -1.18 (0.30), residues: 300 loop : 0.06 (0.31), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 47 HIS 0.004 0.001 HIS B 111 PHE 0.017 0.001 PHE A 270 TYR 0.013 0.001 TYR B 68 ARG 0.003 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 1.058 Fit side-chains REVERT: A 220 GLU cc_start: 0.7534 (tt0) cc_final: 0.7178 (mt-10) REVERT: A 224 ASP cc_start: 0.8617 (t0) cc_final: 0.8305 (t0) REVERT: A 249 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 280 ARG cc_start: 0.8488 (mtt180) cc_final: 0.7428 (mtt180) REVERT: A 326 MET cc_start: 0.7715 (mmt) cc_final: 0.7144 (mmm) REVERT: A 379 LYS cc_start: 0.8402 (ttpt) cc_final: 0.8184 (tttp) REVERT: A 422 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8620 (mmtm) REVERT: A 425 TYR cc_start: 0.8519 (t80) cc_final: 0.6977 (t80) REVERT: A 437 GLN cc_start: 0.8539 (mt0) cc_final: 0.8179 (tt0) REVERT: B 168 GLU cc_start: 0.8437 (mp0) cc_final: 0.8101 (pm20) REVERT: B 220 GLU cc_start: 0.7453 (tt0) cc_final: 0.6935 (mt-10) REVERT: B 249 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7237 (tt0) REVERT: B 262 LEU cc_start: 0.9204 (mp) cc_final: 0.8755 (mp) REVERT: B 275 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 314 GLU cc_start: 0.7445 (mp0) cc_final: 0.7075 (mp0) REVERT: B 326 MET cc_start: 0.7698 (mmt) cc_final: 0.7368 (mmt) REVERT: B 420 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 437 GLN cc_start: 0.8751 (mt0) cc_final: 0.8522 (mt0) REVERT: C 60 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8186 (mm) REVERT: C 275 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8029 (p) REVERT: C 326 MET cc_start: 0.7924 (mmt) cc_final: 0.7518 (mmt) outliers start: 41 outliers final: 34 residues processed: 236 average time/residue: 0.1805 time to fit residues: 62.1963 Evaluate side-chains 249 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 445 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 83 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 0.0020 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9888 Z= 0.161 Angle : 0.565 7.744 13458 Z= 0.284 Chirality : 0.042 0.317 1512 Planarity : 0.003 0.036 1749 Dihedral : 4.298 20.098 1500 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.86 % Allowed : 23.04 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.36 (0.26), residues: 1266 helix: 1.40 (0.26), residues: 444 sheet: -0.99 (0.31), residues: 297 loop : 0.17 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 47 HIS 0.003 0.001 HIS C 111 PHE 0.014 0.001 PHE A 270 TYR 0.010 0.001 TYR B 457 ARG 0.006 0.000 ARG B 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 220 GLU cc_start: 0.7516 (tt0) cc_final: 0.7160 (mt-10) REVERT: A 249 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 326 MET cc_start: 0.7682 (mmt) cc_final: 0.7103 (mmm) REVERT: A 425 TYR cc_start: 0.8485 (t80) cc_final: 0.7103 (t80) REVERT: B 168 GLU cc_start: 0.8419 (mp0) cc_final: 0.8150 (pm20) REVERT: B 220 GLU cc_start: 0.7411 (tt0) cc_final: 0.6871 (mt-10) REVERT: B 249 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7229 (tt0) REVERT: B 262 LEU cc_start: 0.9182 (mp) cc_final: 0.8791 (mp) REVERT: B 275 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 314 GLU cc_start: 0.7439 (mp0) cc_final: 0.7079 (mp0) REVERT: B 326 MET cc_start: 0.7690 (mmt) cc_final: 0.7322 (mmt) REVERT: B 403 ASN cc_start: 0.8858 (m-40) cc_final: 0.8542 (m110) REVERT: B 420 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 437 GLN cc_start: 0.8720 (mt0) cc_final: 0.8509 (mt0) REVERT: C 60 LEU cc_start: 0.8595 (tt) cc_final: 0.8183 (mm) REVERT: C 278 GLU cc_start: 0.8396 (tt0) cc_final: 0.7922 (tt0) REVERT: C 326 MET cc_start: 0.7925 (mmt) cc_final: 0.7530 (mmt) outliers start: 36 outliers final: 30 residues processed: 246 average time/residue: 0.1861 time to fit residues: 66.6908 Evaluate side-chains 248 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 217 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 249 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 445 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.160554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137280 restraints weight = 16546.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141308 restraints weight = 9271.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144088 restraints weight = 6221.018| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9888 Z= 0.176 Angle : 0.577 7.949 13458 Z= 0.288 Chirality : 0.042 0.317 1512 Planarity : 0.003 0.037 1749 Dihedral : 4.211 19.997 1500 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.43 % Allowed : 23.26 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1266 helix: 1.47 (0.26), residues: 444 sheet: -0.94 (0.31), residues: 297 loop : 0.20 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 47 HIS 0.002 0.001 HIS C 111 PHE 0.010 0.001 PHE B 93 TYR 0.010 0.001 TYR C 230 ARG 0.004 0.000 ARG B 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2238.53 seconds wall clock time: 41 minutes 44.99 seconds (2504.99 seconds total)