Starting phenix.real_space_refine on Sat Dec 9 01:23:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/12_2023/6ave_7009.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/12_2023/6ave_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_7009/12_2023/6ave_7009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/12_2023/6ave_7009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/12_2023/6ave_7009.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ave_7009/12_2023/6ave_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-1.21rc1-5172/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: 5.86, per 1000 atoms: 0.61 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: 4.14 Conformation dependent library (CDL) restraints added in 1.9 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: 1.31 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: 2.93 Time building geometry restraints manager: 4.49 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.250 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.070 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- 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 : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.2527 time to fit residues: 143.4100 Evaluate side-chains 239 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5678 ------------------------------------------------------------------------------- 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: 1.9990 chunk 95 optimal weight: 0.0020 chunk 52 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.0170 chunk 114 optimal weight: 4.9990 overall best weight: 0.2666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 261 GLN A 277 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN B 261 GLN B 403 ASN C 249 GLN C 277 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9888 Z= 0.199 Angle : 0.666 7.628 13458 Z= 0.349 Chirality : 0.047 0.458 1512 Planarity : 0.004 0.035 1749 Dihedral : 6.431 42.248 1500 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.22 % Allowed : 15.86 % Favored : 80.92 % 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: -1.57 (0.23), residues: 1266 helix: -0.66 (0.22), residues: 441 sheet: -1.36 (0.29), residues: 291 loop : -0.97 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.008 0.001 HIS C 328 PHE 0.021 0.002 PHE B 270 TYR 0.015 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 311 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 281 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 299 average time/residue: 0.1857 time to fit residues: 80.0973 Evaluate side-chains 241 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1264 time to fit residues: 3.9945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 227 GLN ** B 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 HIS C 227 GLN C 249 GLN C 403 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3382 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= 0.192 Angle : 0.590 7.275 13458 Z= 0.310 Chirality : 0.044 0.390 1512 Planarity : 0.004 0.033 1749 Dihedral : 5.514 33.049 1500 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.57 % Allowed : 21.54 % Favored : 75.88 % 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: -0.73 (0.24), residues: 1266 helix: 0.37 (0.25), residues: 441 sheet: -1.26 (0.30), residues: 264 loop : -0.62 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS B 111 PHE 0.016 0.001 PHE B 270 TYR 0.019 0.001 TYR A 68 ARG 0.009 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 291 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 267 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 278 average time/residue: 0.1992 time to fit residues: 80.7771 Evaluate side-chains 231 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 219 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1193 time to fit residues: 4.6630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.0970 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.3582 ------------------------------------------------------------------------------- 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** C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9888 Z= 0.337 Angle : 0.653 8.648 13458 Z= 0.334 Chirality : 0.045 0.366 1512 Planarity : 0.004 0.028 1749 Dihedral : 5.382 26.283 1500 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.04 % Allowed : 23.79 % Favored : 74.17 % 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: -0.48 (0.25), residues: 1266 helix: 0.48 (0.25), residues: 459 sheet: -1.33 (0.30), residues: 267 loop : -0.28 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 288 HIS 0.008 0.002 HIS A 111 PHE 0.017 0.002 PHE A 270 TYR 0.020 0.002 TYR B 68 ARG 0.005 0.001 ARG A 280 *********************** 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 247 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 237 average time/residue: 0.1950 time to fit residues: 66.8704 Evaluate side-chains 234 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 219 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1070 time to fit residues: 4.3897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.0030 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.0170 chunk 109 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9888 Z= 0.212 Angle : 0.577 7.942 13458 Z= 0.301 Chirality : 0.043 0.348 1512 Planarity : 0.003 0.028 1749 Dihedral : 4.917 24.095 1500 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.47 % Allowed : 23.90 % 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: -0.10 (0.25), residues: 1266 helix: 1.07 (0.26), residues: 441 sheet: -1.04 (0.31), residues: 270 loop : -0.36 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.004 0.001 HIS C 111 PHE 0.015 0.001 PHE A 270 TYR 0.021 0.001 TYR A 68 ARG 0.003 0.000 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 251 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 1.138 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 241 average time/residue: 0.2015 time to fit residues: 71.0630 Evaluate side-chains 228 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 215 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0990 time to fit residues: 3.9262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9888 Z= 0.197 Angle : 0.575 10.532 13458 Z= 0.293 Chirality : 0.043 0.341 1512 Planarity : 0.003 0.028 1749 Dihedral : 4.744 23.843 1500 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.50 % Allowed : 24.33 % Favored : 74.17 % 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: 0.10 (0.25), residues: 1266 helix: 1.24 (0.26), residues: 444 sheet: -0.92 (0.32), residues: 273 loop : -0.24 (0.30), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.003 0.001 HIS B 111 PHE 0.013 0.001 PHE A 300 TYR 0.017 0.001 TYR A 68 ARG 0.003 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 233 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 219 time to evaluate : 1.785 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 225 average time/residue: 0.2146 time to fit residues: 71.0392 Evaluate side-chains 216 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 206 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0961 time to fit residues: 3.2383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN A 437 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4347 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= 0.225 Angle : 0.586 8.762 13458 Z= 0.300 Chirality : 0.043 0.332 1512 Planarity : 0.004 0.029 1749 Dihedral : 4.614 22.778 1500 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.57 % Allowed : 23.37 % Favored : 74.06 % 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: 0.23 (0.25), residues: 1266 helix: 1.52 (0.26), residues: 426 sheet: -0.83 (0.30), residues: 291 loop : -0.25 (0.30), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.004 0.001 HIS B 111 PHE 0.013 0.001 PHE A 300 TYR 0.019 0.001 TYR A 68 ARG 0.004 0.000 ARG A 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 247 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 223 time to evaluate : 1.028 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 231 average time/residue: 0.1850 time to fit residues: 62.2066 Evaluate side-chains 229 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1039 time to fit residues: 4.7377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 277 GLN C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9888 Z= 0.201 Angle : 0.583 9.083 13458 Z= 0.298 Chirality : 0.043 0.328 1512 Planarity : 0.004 0.039 1749 Dihedral : 4.517 22.378 1500 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.75 % Allowed : 24.97 % Favored : 74.28 % 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: 0.25 (0.26), residues: 1266 helix: 1.19 (0.26), residues: 447 sheet: -0.79 (0.32), residues: 273 loop : -0.02 (0.30), residues: 546 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 0.013 0.001 PHE A 300 TYR 0.018 0.001 TYR A 68 ARG 0.004 0.000 ARG A 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 220 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 213 time to evaluate : 1.083 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 217 average time/residue: 0.1831 time to fit residues: 58.4537 Evaluate side-chains 217 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 212 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0887 time to fit residues: 2.2988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.3980 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 88 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9888 Z= 0.161 Angle : 0.584 9.455 13458 Z= 0.296 Chirality : 0.042 0.327 1512 Planarity : 0.004 0.036 1749 Dihedral : 4.295 20.564 1500 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.43 % Allowed : 25.40 % Favored : 74.17 % 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: 0.38 (0.26), residues: 1266 helix: 1.34 (0.26), residues: 441 sheet: -0.66 (0.32), residues: 273 loop : -0.01 (0.30), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.002 0.001 HIS B 111 PHE 0.014 0.001 PHE B 300 TYR 0.021 0.001 TYR A 68 ARG 0.004 0.000 ARG A 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 231 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 227 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 229 average time/residue: 0.1879 time to fit residues: 62.7380 Evaluate side-chains 217 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0848 time to fit residues: 1.6573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9888 Z= 0.223 Angle : 0.602 8.191 13458 Z= 0.307 Chirality : 0.043 0.325 1512 Planarity : 0.004 0.035 1749 Dihedral : 4.314 22.017 1500 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.11 % Allowed : 26.90 % Favored : 72.99 % 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: 0.38 (0.26), residues: 1266 helix: 1.22 (0.26), residues: 444 sheet: -0.66 (0.32), residues: 273 loop : 0.10 (0.30), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 288 HIS 0.004 0.001 HIS B 111 PHE 0.017 0.001 PHE A 270 TYR 0.015 0.001 TYR B 399 ARG 0.004 0.000 ARG A 310 ********************** 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 221 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 221 average time/residue: 0.1837 time to fit residues: 59.9527 Evaluate side-chains 217 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1292 time to fit residues: 1.8091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.161917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137862 restraints weight = 16556.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141880 restraints weight = 9523.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144677 restraints weight = 6494.402| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9888 Z= 0.189 Angle : 0.600 9.615 13458 Z= 0.305 Chirality : 0.043 0.323 1512 Planarity : 0.004 0.035 1749 Dihedral : 4.248 20.267 1500 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.43 % Allowed : 26.80 % Favored : 72.78 % 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: 1.19 (0.26), residues: 447 sheet: -0.62 (0.32), residues: 273 loop : 0.06 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.003 0.001 HIS B 111 PHE 0.013 0.001 PHE A 300 TYR 0.016 0.001 TYR A 68 ARG 0.004 0.000 ARG A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.97 seconds wall clock time: 41 minutes 10.42 seconds (2470.42 seconds total)