Starting phenix.real_space_refine on Fri Sep 27 04:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxq_38758/09_2024/8xxq_38758.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxq_38758/09_2024/8xxq_38758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxq_38758/09_2024/8xxq_38758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxq_38758/09_2024/8xxq_38758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxq_38758/09_2024/8xxq_38758.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xxq_38758/09_2024/8xxq_38758.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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 104 5.16 5 C 9620 2.51 5 N 2608 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15172 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3793 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3793 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "C" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3793 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Chain: "D" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3793 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 29, 'TRANS': 469} Time building chain proxies: 9.82, per 1000 atoms: 0.65 Number of scatterers: 15172 At special positions: 0 Unit cell: (108.712, 107, 101.864, 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 104 16.00 O 2840 8.00 N 2608 7.00 C 9620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.2 seconds 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 46.0% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 43 through 64 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 157 through 170 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.514A pdb=" N THR A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.675A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.783A pdb=" N HIS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 296 through 299 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 328 through 345 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'B' and resid 43 through 64 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 157 through 170 Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.465A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.740A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.772A pdb=" N HIS B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 328 through 345 Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 466 through 474 removed outlier: 3.583A pdb=" N TYR B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'C' and resid 43 through 64 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 65 through 83 Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 98 through 117 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 157 through 170 Proline residue: C 165 - end of helix removed outlier: 3.616A pdb=" N CYS C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.491A pdb=" N THR C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.679A pdb=" N HIS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 279 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 296 through 299 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 328 through 345 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.547A pdb=" N TYR C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'D' and resid 43 through 64 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 65 through 83 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 98 through 117 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 157 through 170 Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.477A pdb=" N THR D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.819A pdb=" N HIS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 296 through 299 Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 328 through 345 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 467 through 474 Processing helix chain 'D' and resid 485 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 132 removed outlier: 3.851A pdb=" N GLU A 126 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET A 135 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS B 257 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N PHE B 418 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 259 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B 258 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 294 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 260 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA B 291 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR B 396 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 293 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 371 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.669A pdb=" N CYS A 147 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS A 177 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A 149 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 146 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 225 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 148 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE A 227 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 150 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS A 223 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N GLN A 249 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 225 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ASN A 251 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 227 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 351 removed outlier: 6.496A pdb=" N ILE A 371 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY A 258 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 294 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 260 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A 257 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE A 418 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 259 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 437 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLN B 483 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 439 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 126 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'B' and resid 24 through 28 Processing sheet with id=AA8, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.313A pdb=" N PHE B 174 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 146 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 224 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS B 223 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLN B 249 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 225 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASN B 251 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE B 227 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 28 Processing sheet with id=AB2, first strand: chain 'C' and resid 127 through 132 removed outlier: 6.577A pdb=" N MET C 135 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N HIS D 257 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N PHE D 418 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 259 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY D 258 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 294 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 260 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA D 291 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR D 396 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU D 293 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE D 371 " --> pdb=" O LEU D 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 203 through 205 removed outlier: 6.312A pdb=" N PHE C 174 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS C 147 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LYS C 177 " --> pdb=" O CYS C 147 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY C 149 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL C 146 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE C 225 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 148 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE C 227 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 150 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 348 through 351 removed outlier: 6.502A pdb=" N ILE C 371 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA C 291 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 396 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 293 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY C 258 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 294 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL C 260 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS C 257 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE C 418 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 259 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 437 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLN D 483 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL C 439 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET D 135 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 137 " --> pdb=" O MET D 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'D' and resid 24 through 28 Processing sheet with id=AB7, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.381A pdb=" N PHE D 174 " --> pdb=" O ASN D 204 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS D 147 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LYS D 177 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY D 149 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL D 146 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA D 224 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS D 223 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLN D 249 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE D 225 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASN D 251 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE D 227 " --> pdb=" O ASN D 251 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 2124 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: 5.27 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5023 1.34 - 1.46: 3064 1.46 - 1.58: 7217 1.58 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 15480 Sorted by residual: bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N SER B 3 " pdb=" CA SER B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N SER D 3 " pdb=" CA SER D 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N SER C 3 " pdb=" CA SER C 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ARG D 456 " pdb=" CA ARG D 456 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.17e-02 7.31e+03 2.45e+00 ... (remaining 15475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 20435 1.16 - 2.32: 387 2.32 - 3.47: 107 3.47 - 4.63: 54 4.63 - 5.79: 5 Bond angle restraints: 20988 Sorted by residual: angle pdb=" C SER D 455 " pdb=" N ARG D 456 " pdb=" CA ARG D 456 " ideal model delta sigma weight residual 121.19 126.53 -5.34 1.59e+00 3.96e-01 1.13e+01 angle pdb=" C SER B 455 " pdb=" N ARG B 456 " pdb=" CA ARG B 456 " ideal model delta sigma weight residual 120.79 124.93 -4.14 1.39e+00 5.18e-01 8.87e+00 angle pdb=" C SER C 455 " pdb=" N ARG C 456 " pdb=" CA ARG C 456 " ideal model delta sigma weight residual 120.79 124.74 -3.95 1.39e+00 5.18e-01 8.07e+00 angle pdb=" CA GLN B 209 " pdb=" C GLN B 209 " pdb=" O GLN B 209 " ideal model delta sigma weight residual 121.50 118.02 3.48 1.25e+00 6.40e-01 7.74e+00 angle pdb=" C ARG C 456 " pdb=" CA ARG C 456 " pdb=" CB ARG C 456 " ideal model delta sigma weight residual 110.92 115.32 -4.40 1.59e+00 3.96e-01 7.65e+00 ... (remaining 20983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 9087 16.09 - 32.19: 221 32.19 - 48.28: 67 48.28 - 64.37: 2 64.37 - 80.46: 3 Dihedral angle restraints: 9380 sinusoidal: 3700 harmonic: 5680 Sorted by residual: dihedral pdb=" CA GLY D 454 " pdb=" C GLY D 454 " pdb=" N SER D 455 " pdb=" CA SER D 455 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LEU D 161 " pdb=" C LEU D 161 " pdb=" N TRP D 162 " pdb=" CA TRP D 162 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 dihedral pdb=" N PHE D 465 " pdb=" CA PHE D 465 " pdb=" CB PHE D 465 " pdb=" CG PHE D 465 " ideal model delta sinusoidal sigma weight residual -60.00 -112.23 52.23 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1504 0.027 - 0.054: 528 0.054 - 0.081: 141 0.081 - 0.108: 130 0.108 - 0.135: 85 Chirality restraints: 2388 Sorted by residual: chirality pdb=" CA VAL C 5 " pdb=" N VAL C 5 " pdb=" C VAL C 5 " pdb=" CB VAL C 5 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL D 441 " pdb=" N VAL D 441 " pdb=" C VAL D 441 " pdb=" CB VAL D 441 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL C 441 " pdb=" N VAL C 441 " pdb=" C VAL C 441 " pdb=" CB VAL C 441 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 2385 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 159 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 160 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 159 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO C 160 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 159 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO D 160 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " 0.016 5.00e-02 4.00e+02 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 286 2.69 - 3.25: 15580 3.25 - 3.80: 25034 3.80 - 4.35: 34175 4.35 - 4.90: 56264 Nonbonded interactions: 131339 Sorted by model distance: nonbonded pdb=" OD2 ASP A 462 " pdb=" OG1 THR B 463 " model vdw 2.142 3.040 nonbonded pdb=" OD1 ASN C 464 " pdb=" NE2 GLN C 469 " model vdw 2.153 3.120 nonbonded pdb=" ND2 ASN B 33 " pdb=" O ASN B 363 " model vdw 2.154 3.120 nonbonded pdb=" OD1 ASN B 464 " pdb=" NE2 GLN B 469 " model vdw 2.154 3.120 nonbonded pdb=" OD2 ASP C 462 " pdb=" OG1 THR D 463 " model vdw 2.161 3.040 ... (remaining 131334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.110 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.002 0.033 15480 Z= 0.127 Angle : 0.480 5.790 20988 Z= 0.273 Chirality : 0.041 0.135 2388 Planarity : 0.003 0.031 2732 Dihedral : 8.138 80.464 5732 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % Rotamer: Outliers : 0.43 % Allowed : 1.58 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1988 helix: 1.10 (0.18), residues: 812 sheet: -0.64 (0.25), residues: 396 loop : -1.07 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 484 HIS 0.002 0.000 HIS B 115 PHE 0.014 0.001 PHE D 164 TYR 0.006 0.001 TYR A 76 ARG 0.002 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 254 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 501 MET cc_start: 0.0563 (mtm) cc_final: -0.0432 (mtp) outliers start: 7 outliers final: 1 residues processed: 261 average time/residue: 1.1973 time to fit residues: 346.3775 Evaluate side-chains 144 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS A 440 ASN B 41 GLN B 115 HIS B 210 HIS B 440 ASN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 115 HIS ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN C 413 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 115 HIS D 409 ASN D 440 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15480 Z= 0.267 Angle : 0.582 8.998 20988 Z= 0.293 Chirality : 0.046 0.184 2388 Planarity : 0.004 0.037 2732 Dihedral : 4.128 34.866 2102 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.01 % Allowed : 9.43 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 1988 helix: 1.63 (0.18), residues: 836 sheet: -0.19 (0.27), residues: 368 loop : -0.25 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 162 HIS 0.003 0.001 HIS C 307 PHE 0.020 0.002 PHE D 164 TYR 0.015 0.002 TYR A 466 ARG 0.008 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 486 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7156 (tm-30) REVERT: B 501 MET cc_start: 0.0328 (mtm) cc_final: -0.0789 (mtp) REVERT: C 486 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7368 (tm-30) REVERT: D 486 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7347 (tm-30) outliers start: 33 outliers final: 7 residues processed: 159 average time/residue: 1.1951 time to fit residues: 211.9614 Evaluate side-chains 124 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 272 GLN B 77 GLN B 172 ASN B 231 ASN B 469 GLN B 483 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 GLN D 77 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15480 Z= 0.364 Angle : 0.602 8.013 20988 Z= 0.305 Chirality : 0.047 0.197 2388 Planarity : 0.004 0.038 2732 Dihedral : 4.417 21.528 2100 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.74 % Allowed : 9.37 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1988 helix: 1.72 (0.18), residues: 836 sheet: 0.02 (0.27), residues: 368 loop : -0.04 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 162 HIS 0.003 0.001 HIS A 219 PHE 0.018 0.002 PHE C 164 TYR 0.021 0.002 TYR A 466 ARG 0.005 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 126 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7359 (tm-30) REVERT: B 81 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8292 (mttm) REVERT: B 486 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 501 MET cc_start: 0.0486 (mtm) cc_final: -0.0573 (mtp) REVERT: C 486 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7305 (tm-30) REVERT: D 486 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7396 (tm-30) outliers start: 45 outliers final: 18 residues processed: 162 average time/residue: 1.1695 time to fit residues: 211.4834 Evaluate side-chains 134 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 77 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15480 Z= 0.219 Angle : 0.558 10.401 20988 Z= 0.277 Chirality : 0.045 0.184 2388 Planarity : 0.004 0.036 2732 Dihedral : 4.301 22.618 2100 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.82 % Allowed : 11.19 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1988 helix: 1.87 (0.18), residues: 840 sheet: 0.15 (0.27), residues: 356 loop : 0.05 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 484 HIS 0.003 0.001 HIS A 219 PHE 0.018 0.001 PHE B 164 TYR 0.018 0.001 TYR C 466 ARG 0.004 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7352 (tm-30) REVERT: B 81 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8420 (mttm) REVERT: B 486 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7382 (tm-30) REVERT: B 501 MET cc_start: 0.0641 (mtm) cc_final: -0.0448 (mtp) REVERT: C 486 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7387 (tm-30) REVERT: D 411 TYR cc_start: 0.8540 (m-80) cc_final: 0.8297 (m-80) REVERT: D 486 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7368 (tm-30) outliers start: 30 outliers final: 11 residues processed: 150 average time/residue: 1.2449 time to fit residues: 208.4201 Evaluate side-chains 133 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 409 ASN C 77 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 231 ASN D 272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15480 Z= 0.354 Angle : 0.616 9.738 20988 Z= 0.306 Chirality : 0.046 0.201 2388 Planarity : 0.004 0.036 2732 Dihedral : 4.475 25.692 2100 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 11.62 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1988 helix: 1.82 (0.18), residues: 840 sheet: 0.14 (0.27), residues: 356 loop : 0.02 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 484 HIS 0.003 0.001 HIS B 257 PHE 0.019 0.002 PHE B 164 TYR 0.020 0.002 TYR C 466 ARG 0.004 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8079 (tpp) REVERT: A 486 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 501 MET cc_start: 0.0776 (mtm) cc_final: -0.0375 (mtp) REVERT: C 486 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7427 (tm-30) REVERT: D 411 TYR cc_start: 0.8640 (m-80) cc_final: 0.8432 (m-80) REVERT: D 486 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7413 (tm-30) outliers start: 38 outliers final: 17 residues processed: 148 average time/residue: 1.1275 time to fit residues: 187.3876 Evaluate side-chains 129 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 8.9990 chunk 170 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN C 77 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN C 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15480 Z= 0.339 Angle : 0.618 10.320 20988 Z= 0.305 Chirality : 0.047 0.201 2388 Planarity : 0.004 0.035 2732 Dihedral : 4.528 26.753 2100 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.13 % Allowed : 12.04 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1988 helix: 1.80 (0.18), residues: 840 sheet: 0.15 (0.28), residues: 356 loop : 0.01 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 484 HIS 0.003 0.001 HIS B 257 PHE 0.019 0.001 PHE B 164 TYR 0.020 0.002 TYR C 466 ARG 0.003 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 1.832 Fit side-chains REVERT: A 486 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7320 (tm-30) REVERT: B 81 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8314 (mttm) REVERT: B 486 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 501 MET cc_start: 0.0680 (mtm) cc_final: -0.0661 (mtp) REVERT: C 486 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7334 (tm-30) REVERT: C 488 ASP cc_start: 0.7317 (m-30) cc_final: 0.7115 (m-30) REVERT: D 411 TYR cc_start: 0.8663 (m-80) cc_final: 0.8443 (m-80) REVERT: D 486 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7279 (tm-30) REVERT: D 488 ASP cc_start: 0.7227 (m-30) cc_final: 0.7010 (m-30) REVERT: D 498 MET cc_start: -0.1017 (mmp) cc_final: -0.1527 (tpp) outliers start: 35 outliers final: 19 residues processed: 143 average time/residue: 1.1242 time to fit residues: 180.1522 Evaluate side-chains 130 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15480 Z= 0.157 Angle : 0.577 13.110 20988 Z= 0.278 Chirality : 0.044 0.192 2388 Planarity : 0.004 0.032 2732 Dihedral : 4.282 21.337 2100 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.70 % Allowed : 12.47 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 1988 helix: 1.95 (0.18), residues: 840 sheet: 0.15 (0.27), residues: 356 loop : 0.07 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 24 HIS 0.003 0.001 HIS A 115 PHE 0.017 0.001 PHE B 164 TYR 0.014 0.001 TYR C 466 ARG 0.003 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.902 Fit side-chains REVERT: A 486 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 81 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8273 (mttm) REVERT: B 486 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 501 MET cc_start: 0.0642 (mtm) cc_final: -0.0798 (mtp) REVERT: C 486 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7296 (tm-30) REVERT: D 411 TYR cc_start: 0.8620 (m-80) cc_final: 0.8364 (m-80) REVERT: D 486 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7257 (tm-30) REVERT: D 488 ASP cc_start: 0.7138 (m-30) cc_final: 0.6902 (m-30) REVERT: D 498 MET cc_start: -0.1247 (mmp) cc_final: -0.1861 (tpp) outliers start: 28 outliers final: 14 residues processed: 147 average time/residue: 1.1548 time to fit residues: 192.6419 Evaluate side-chains 136 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15480 Z= 0.323 Angle : 0.627 10.990 20988 Z= 0.306 Chirality : 0.046 0.198 2388 Planarity : 0.004 0.035 2732 Dihedral : 4.429 25.253 2100 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.58 % Allowed : 12.59 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 1988 helix: 1.92 (0.18), residues: 840 sheet: 0.15 (0.28), residues: 356 loop : 0.05 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 24 HIS 0.003 0.001 HIS B 257 PHE 0.022 0.001 PHE C 164 TYR 0.018 0.002 TYR C 466 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 1.875 Fit side-chains REVERT: A 486 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7311 (tm-30) REVERT: B 81 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8333 (mttm) REVERT: B 486 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 501 MET cc_start: 0.0623 (mtm) cc_final: -0.0894 (mtp) REVERT: C 486 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7335 (tm-30) REVERT: D 486 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7296 (tm-30) REVERT: D 498 MET cc_start: -0.1080 (mmp) cc_final: -0.1809 (tpp) outliers start: 26 outliers final: 15 residues processed: 138 average time/residue: 1.1691 time to fit residues: 180.5191 Evaluate side-chains 127 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15480 Z= 0.182 Angle : 0.597 12.573 20988 Z= 0.289 Chirality : 0.045 0.173 2388 Planarity : 0.004 0.031 2732 Dihedral : 4.329 22.162 2100 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.40 % Allowed : 12.47 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1988 helix: 1.94 (0.18), residues: 840 sheet: 0.14 (0.28), residues: 356 loop : 0.06 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 162 HIS 0.003 0.001 HIS A 219 PHE 0.020 0.001 PHE A 164 TYR 0.018 0.002 TYR A 76 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.839 Fit side-chains REVERT: A 486 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 81 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8306 (mttm) REVERT: B 486 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7405 (tm-30) REVERT: B 501 MET cc_start: 0.0719 (mtm) cc_final: -0.0783 (mtp) REVERT: C 486 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7291 (tm-30) REVERT: D 486 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 488 ASP cc_start: 0.7079 (m-30) cc_final: 0.6842 (m-30) REVERT: D 498 MET cc_start: -0.1109 (mmp) cc_final: -0.2159 (tpp) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 1.1942 time to fit residues: 182.8970 Evaluate side-chains 133 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9980 chunk 186 optimal weight: 0.0970 chunk 113 optimal weight: 0.0970 chunk 88 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 179 optimal weight: 0.0060 chunk 155 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN D 272 GLN D 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15480 Z= 0.144 Angle : 0.584 10.691 20988 Z= 0.282 Chirality : 0.044 0.168 2388 Planarity : 0.004 0.031 2732 Dihedral : 4.198 19.435 2100 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.97 % Allowed : 13.14 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1988 helix: 1.97 (0.18), residues: 840 sheet: 0.14 (0.27), residues: 356 loop : 0.09 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 162 HIS 0.002 0.001 HIS C 307 PHE 0.019 0.001 PHE A 164 TYR 0.016 0.001 TYR D 76 ARG 0.008 0.000 ARG A 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3976 Ramachandran restraints generated. 1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.824 Fit side-chains REVERT: A 486 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7234 (tm-30) REVERT: B 486 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 501 MET cc_start: 0.0636 (mtm) cc_final: -0.0947 (mtp) REVERT: C 486 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 486 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7155 (tm-30) REVERT: D 488 ASP cc_start: 0.6976 (m-30) cc_final: 0.6761 (m-30) REVERT: D 498 MET cc_start: -0.1196 (mmp) cc_final: -0.2287 (tpp) outliers start: 16 outliers final: 9 residues processed: 148 average time/residue: 1.1114 time to fit residues: 185.4661 Evaluate side-chains 132 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 458 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.083480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068514 restraints weight = 41602.164| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 4.20 r_work: 0.2996 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15480 Z= 0.222 Angle : 0.615 9.411 20988 Z= 0.303 Chirality : 0.045 0.184 2388 Planarity : 0.004 0.030 2732 Dihedral : 4.241 21.474 2100 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.34 % Allowed : 12.83 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1988 helix: 1.93 (0.18), residues: 840 sheet: 0.06 (0.27), residues: 368 loop : 0.24 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 162 HIS 0.003 0.001 HIS B 257 PHE 0.019 0.001 PHE C 164 TYR 0.018 0.002 TYR A 76 ARG 0.003 0.000 ARG C 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4321.88 seconds wall clock time: 77 minutes 35.40 seconds (4655.40 seconds total)