Starting phenix.real_space_refine on Sun Apr 5 14:12:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydi_33748/04_2026/7ydi_33748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydi_33748/04_2026/7ydi_33748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ydi_33748/04_2026/7ydi_33748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydi_33748/04_2026/7ydi_33748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ydi_33748/04_2026/7ydi_33748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydi_33748/04_2026/7ydi_33748.map" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1490 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 50 5.16 5 C 6144 2.51 5 N 1602 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4864 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1530 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 182} Chain: "H" Number of atoms: 1667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.62, per 1000 atoms: 0.27 Number of scatterers: 9675 At special positions: 0 Unit cell: (108.416, 160.512, 95.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 50 16.00 O 1878 8.00 N 1602 7.00 C 6144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS H 151 " - pdb=" SG ACYS H 207 " distance=2.03 Simple disulfide: pdb=" SG BCYS H 151 " - pdb=" SG BCYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 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 Links applied NAG-ASN " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 53 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 546 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 634.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 35.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 83 removed outlier: 3.802A pdb=" N TYR A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.726A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.750A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.975A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.535A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.703A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.800A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.902A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.582A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.667A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.852A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.039A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.512A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.206A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.736A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.676A pdb=" N ASP A 615 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 372 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.594A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'L' and resid 127 through 133 removed outlier: 3.717A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 4.091A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.571A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.177A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 361 through 362 removed outlier: 7.476A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.511A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.520A pdb=" N GLU H 10 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR H 121 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.548A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS H 151 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 162 through 165 removed outlier: 4.743A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN H 210 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER H 164 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN H 208 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR H 205 " --> pdb=" O VAL H 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL H 209 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H 218 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR H 216 " --> pdb=" O HIS H 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.980A pdb=" N ALA L 86 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP L 87 " --> pdb=" O GLN L 40 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN L 40 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.980A pdb=" N ALA L 86 " --> pdb=" O LEU L 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 23 Processing sheet with id=AB5, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.176A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE L 141 " --> pdb=" O ALA L 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA L 179 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP L 143 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.646A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS L 154 " --> pdb=" O SER L 197 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER L 197 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1071 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: 1.29 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3101 1.35 - 1.46: 2498 1.46 - 1.58: 4259 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9931 Sorted by residual: bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG A 904 " pdb=" O5 NAG A 904 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C GLU H 159 " pdb=" N PRO H 160 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.11e+00 bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" CB GLN H 65 " pdb=" CG GLN H 65 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.18e+00 ... (remaining 9926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 13284 2.32 - 4.65: 183 4.65 - 6.97: 36 6.97 - 9.29: 13 9.29 - 11.62: 3 Bond angle restraints: 13519 Sorted by residual: angle pdb=" CB MET A 557 " pdb=" CG MET A 557 " pdb=" SD MET A 557 " ideal model delta sigma weight residual 112.70 124.32 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA GLU A 110 " pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA MET A 82 " pdb=" CB MET A 82 " pdb=" CG MET A 82 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET A 332 " pdb=" CG MET A 332 " pdb=" SD MET A 332 " ideal model delta sigma weight residual 112.70 123.39 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CB LYS E 458 " pdb=" CG LYS E 458 " pdb=" CD LYS E 458 " ideal model delta sigma weight residual 111.30 119.23 -7.93 2.30e+00 1.89e-01 1.19e+01 ... (remaining 13514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5333 17.87 - 35.74: 455 35.74 - 53.61: 126 53.61 - 71.47: 18 71.47 - 89.34: 9 Dihedral angle restraints: 5941 sinusoidal: 2365 harmonic: 3576 Sorted by residual: dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 198 " pdb=" CB CYS L 198 " ideal model delta sinusoidal sigma weight residual 93.00 139.36 -46.36 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -47.98 -38.02 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CA ILE H 51 " pdb=" C ILE H 51 " pdb=" N ILE H 52 " pdb=" CA ILE H 52 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1310 0.073 - 0.145: 155 0.145 - 0.218: 3 0.218 - 0.290: 1 0.290 - 0.363: 1 Chirality restraints: 1470 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB THR A 334 " pdb=" CA THR A 334 " pdb=" OG1 THR A 334 " pdb=" CG2 THR A 334 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 1467 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " 0.022 2.00e-02 2.50e+03 4.38e-02 1.91e+01 pdb=" C GLY L 112 " -0.076 2.00e-02 2.50e+03 pdb=" O GLY L 112 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN L 113 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 159 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO H 160 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 160 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 110 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" CD GLU A 110 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU A 110 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 110 " 0.014 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 61 2.53 - 3.12: 6859 3.12 - 3.72: 15478 3.72 - 4.31: 20678 4.31 - 4.90: 34224 Nonbonded interactions: 77300 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 901 " model vdw 1.938 2.230 nonbonded pdb=" OE1 GLU H 6 " pdb=" N GLY H 117 " model vdw 2.086 3.120 nonbonded pdb=" O TYR A 515 " pdb=" OG1 THR A 519 " model vdw 2.288 3.040 nonbonded pdb=" O LYS A 114 " pdb=" OG1 THR A 118 " model vdw 2.310 3.040 nonbonded pdb=" O THR E 393 " pdb=" OG1 THR E 523 " model vdw 2.316 3.040 ... (remaining 77295 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 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 : 0.003 0.044 9949 Z= 0.154 Angle : 0.701 11.618 13555 Z= 0.346 Chirality : 0.045 0.363 1470 Planarity : 0.005 0.057 1744 Dihedral : 14.601 89.344 3621 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.67 % Allowed : 20.53 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1223 helix: 0.22 (0.25), residues: 403 sheet: -0.29 (0.38), residues: 186 loop : -1.09 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 346 TYR 0.023 0.001 TYR H 32 PHE 0.014 0.001 PHE E 486 TRP 0.015 0.001 TRP H 47 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9931) covalent geometry : angle 0.69839 (13519) SS BOND : bond 0.00094 ( 12) SS BOND : angle 0.56956 ( 24) hydrogen bonds : bond 0.17796 ( 378) hydrogen bonds : angle 7.02040 ( 1071) metal coordination : bond 0.00064 ( 2) link_NAG-ASN : bond 0.00256 ( 4) link_NAG-ASN : angle 2.19484 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7813 (t80) cc_final: 0.7459 (t80) REVERT: A 45 LEU cc_start: 0.7500 (tp) cc_final: 0.7258 (mt) REVERT: A 49 ASN cc_start: 0.7790 (m-40) cc_final: 0.7234 (m-40) REVERT: A 90 ASN cc_start: 0.5282 (OUTLIER) cc_final: 0.4943 (t0) REVERT: A 121 ASN cc_start: 0.8153 (m-40) cc_final: 0.7819 (m-40) REVERT: A 150 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6657 (mm-30) REVERT: A 198 ASP cc_start: 0.7134 (p0) cc_final: 0.6916 (p0) REVERT: A 213 ASP cc_start: 0.7902 (p0) cc_final: 0.7583 (m-30) REVERT: A 245 ARG cc_start: 0.5956 (ttp-170) cc_final: 0.5477 (ttp80) REVERT: A 323 MET cc_start: 0.8302 (mmm) cc_final: 0.7989 (mmm) REVERT: A 328 TRP cc_start: 0.7696 (m100) cc_final: 0.6868 (m100) REVERT: A 330 ASN cc_start: 0.8205 (t0) cc_final: 0.7969 (t0) REVERT: A 355 ASP cc_start: 0.7684 (t0) cc_final: 0.6990 (t0) REVERT: A 390 PHE cc_start: 0.6364 (t80) cc_final: 0.6120 (t80) REVERT: A 434 THR cc_start: 0.4862 (p) cc_final: 0.4263 (t) REVERT: A 435 GLU cc_start: 0.6456 (mm-30) cc_final: 0.5501 (pm20) REVERT: A 462 MET cc_start: 0.6783 (ptp) cc_final: 0.6529 (mpp) REVERT: A 471 ASP cc_start: 0.7606 (t0) cc_final: 0.6176 (p0) REVERT: A 472 GLN cc_start: 0.6912 (mt0) cc_final: 0.6485 (tm-30) REVERT: A 480 MET cc_start: 0.7141 (ptm) cc_final: 0.6506 (ptp) REVERT: A 534 LYS cc_start: 0.8030 (mmmm) cc_final: 0.7536 (mmtt) REVERT: A 546 ASN cc_start: 0.5202 (m-40) cc_final: 0.4490 (t0) REVERT: A 582 ARG cc_start: 0.6646 (mmp80) cc_final: 0.5371 (tpm170) REVERT: E 338 PHE cc_start: 0.6314 (m-80) cc_final: 0.5382 (m-80) REVERT: E 406 GLU cc_start: 0.7264 (mp0) cc_final: 0.6814 (mp0) REVERT: E 424 LYS cc_start: 0.7421 (tttm) cc_final: 0.7190 (tttm) REVERT: E 428 ASP cc_start: 0.8414 (p0) cc_final: 0.8186 (p0) REVERT: E 467 ASP cc_start: 0.8139 (t0) cc_final: 0.7853 (t0) REVERT: H 59 ASN cc_start: 0.8435 (p0) cc_final: 0.8047 (p0) REVERT: H 60 TYR cc_start: 0.8523 (m-80) cc_final: 0.8131 (m-10) REVERT: H 65 GLN cc_start: 0.7363 (pm20) cc_final: 0.6687 (tp40) REVERT: H 90 ASP cc_start: 0.7019 (m-30) cc_final: 0.6706 (t0) REVERT: H 94 TYR cc_start: 0.7823 (m-80) cc_final: 0.7604 (m-80) REVERT: H 103 SER cc_start: 0.7853 (OUTLIER) cc_final: 0.6939 (m) REVERT: L 37 TRP cc_start: 0.8188 (m100) cc_final: 0.7884 (m100) REVERT: L 64 PHE cc_start: 0.6393 (m-80) cc_final: 0.5992 (m-80) REVERT: L 87 ASP cc_start: 0.6840 (p0) cc_final: 0.6571 (p0) outliers start: 6 outliers final: 1 residues processed: 283 average time/residue: 0.1032 time to fit residues: 40.3666 Evaluate side-chains 178 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain H residue 103 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN A 81 GLN A 101 GLN A 330 ASN E 394 ASN E 409 GLN E 437 ASN E 506 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.187275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.167854 restraints weight = 21754.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166615 restraints weight = 25132.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.167153 restraints weight = 23259.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.167095 restraints weight = 20241.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167312 restraints weight = 18432.298| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9949 Z= 0.151 Angle : 0.624 8.261 13555 Z= 0.315 Chirality : 0.044 0.177 1470 Planarity : 0.004 0.050 1744 Dihedral : 4.683 56.700 1418 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.09 % Allowed : 18.82 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.24), residues: 1223 helix: 0.50 (0.26), residues: 413 sheet: 0.28 (0.37), residues: 196 loop : -1.02 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 67 TYR 0.015 0.001 TYR A 510 PHE 0.016 0.002 PHE E 497 TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9931) covalent geometry : angle 0.62142 (13519) SS BOND : bond 0.00699 ( 12) SS BOND : angle 0.73922 ( 24) hydrogen bonds : bond 0.03787 ( 378) hydrogen bonds : angle 4.86767 ( 1071) metal coordination : bond 0.00423 ( 2) link_NAG-ASN : bond 0.00238 ( 4) link_NAG-ASN : angle 1.89518 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASN cc_start: 0.7531 (m-40) cc_final: 0.6877 (m-40) REVERT: A 117 ASN cc_start: 0.7928 (p0) cc_final: 0.7477 (p0) REVERT: A 150 GLU cc_start: 0.6654 (tm-30) cc_final: 0.6374 (mm-30) REVERT: A 328 TRP cc_start: 0.8036 (m100) cc_final: 0.6866 (m100) REVERT: A 329 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6443 (tm-30) REVERT: A 355 ASP cc_start: 0.8265 (t0) cc_final: 0.7503 (t0) REVERT: A 359 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7465 (mm) REVERT: A 434 THR cc_start: 0.5631 (p) cc_final: 0.5301 (t) REVERT: A 480 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7660 (ptp) REVERT: A 546 ASN cc_start: 0.3386 (m-40) cc_final: 0.3185 (t0) REVERT: A 582 ARG cc_start: 0.6793 (mmp80) cc_final: 0.6462 (tpm170) REVERT: E 406 GLU cc_start: 0.7914 (mp0) cc_final: 0.7201 (mp0) REVERT: E 418 ILE cc_start: 0.7872 (mt) cc_final: 0.7284 (mt) REVERT: E 467 ASP cc_start: 0.8861 (t0) cc_final: 0.8382 (t0) REVERT: H 59 ASN cc_start: 0.8990 (p0) cc_final: 0.8528 (p0) REVERT: H 60 TYR cc_start: 0.8681 (m-80) cc_final: 0.8388 (m-10) REVERT: L 19 THR cc_start: 0.7370 (m) cc_final: 0.6528 (p) outliers start: 42 outliers final: 14 residues processed: 215 average time/residue: 0.0878 time to fit residues: 27.3003 Evaluate side-chains 160 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 353 TRP Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 182 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN E 409 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 HIS L 16 GLN L 199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.185830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.181764 restraints weight = 20137.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.170685 restraints weight = 33640.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168493 restraints weight = 41675.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168756 restraints weight = 37370.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168799 restraints weight = 27556.247| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9949 Z= 0.126 Angle : 0.571 7.425 13555 Z= 0.288 Chirality : 0.043 0.190 1470 Planarity : 0.004 0.047 1744 Dihedral : 4.160 51.490 1415 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.57 % Allowed : 21.39 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1223 helix: 0.63 (0.27), residues: 412 sheet: 0.27 (0.37), residues: 193 loop : -1.01 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.014 0.001 TYR A 510 PHE 0.028 0.001 PHE H 64 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9931) covalent geometry : angle 0.56710 (13519) SS BOND : bond 0.00364 ( 12) SS BOND : angle 0.78313 ( 24) hydrogen bonds : bond 0.03739 ( 378) hydrogen bonds : angle 4.48761 ( 1071) metal coordination : bond 0.00131 ( 2) link_NAG-ASN : bond 0.00658 ( 4) link_NAG-ASN : angle 2.27045 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7454 (tmm) cc_final: 0.6686 (tmm) REVERT: A 328 TRP cc_start: 0.8152 (m100) cc_final: 0.7496 (m100) REVERT: A 350 ASP cc_start: 0.6557 (t0) cc_final: 0.6257 (p0) REVERT: A 355 ASP cc_start: 0.8342 (t0) cc_final: 0.8031 (t0) REVERT: A 366 MET cc_start: 0.6873 (tpp) cc_final: 0.6285 (mmm) REVERT: A 434 THR cc_start: 0.5753 (p) cc_final: 0.5456 (t) REVERT: A 435 GLU cc_start: 0.7214 (pm20) cc_final: 0.6967 (pm20) REVERT: E 406 GLU cc_start: 0.8100 (mp0) cc_final: 0.7254 (mp0) REVERT: E 467 ASP cc_start: 0.8735 (t0) cc_final: 0.8319 (t0) REVERT: E 524 VAL cc_start: 0.4755 (OUTLIER) cc_final: 0.4480 (m) REVERT: H 60 TYR cc_start: 0.8905 (m-80) cc_final: 0.8568 (m-10) REVERT: L 19 THR cc_start: 0.7219 (m) cc_final: 0.6415 (p) REVERT: L 87 ASP cc_start: 0.7541 (p0) cc_final: 0.7321 (p0) outliers start: 26 outliers final: 16 residues processed: 176 average time/residue: 0.0878 time to fit residues: 22.3742 Evaluate side-chains 153 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 100 optimal weight: 0.0060 chunk 68 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 508 ASN E 360 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN L 199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159214 restraints weight = 33091.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.160891 restraints weight = 48014.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160542 restraints weight = 32374.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160781 restraints weight = 26609.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.160918 restraints weight = 24438.784| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9949 Z= 0.142 Angle : 0.618 12.809 13555 Z= 0.312 Chirality : 0.044 0.344 1470 Planarity : 0.004 0.045 1744 Dihedral : 4.404 50.974 1415 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.18 % Allowed : 20.53 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1223 helix: 0.77 (0.27), residues: 410 sheet: 0.00 (0.34), residues: 211 loop : -0.95 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.017 0.001 TYR E 380 PHE 0.022 0.002 PHE A 555 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9931) covalent geometry : angle 0.60983 (13519) SS BOND : bond 0.00561 ( 12) SS BOND : angle 2.18196 ( 24) hydrogen bonds : bond 0.03682 ( 378) hydrogen bonds : angle 4.36906 ( 1071) metal coordination : bond 0.00066 ( 2) link_NAG-ASN : bond 0.00484 ( 4) link_NAG-ASN : angle 1.89531 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7351 (tmm) cc_final: 0.6917 (tmm) REVERT: A 94 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8330 (tptp) REVERT: A 328 TRP cc_start: 0.8270 (m100) cc_final: 0.7303 (m100) REVERT: A 329 GLU cc_start: 0.6892 (pp20) cc_final: 0.6612 (tm-30) REVERT: A 330 ASN cc_start: 0.8162 (m-40) cc_final: 0.7366 (m-40) REVERT: A 350 ASP cc_start: 0.6960 (t0) cc_final: 0.6670 (p0) REVERT: A 434 THR cc_start: 0.6276 (p) cc_final: 0.6042 (t) REVERT: A 435 GLU cc_start: 0.7031 (pm20) cc_final: 0.6782 (pm20) REVERT: A 479 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: E 406 GLU cc_start: 0.8367 (mp0) cc_final: 0.7546 (mp0) REVERT: E 467 ASP cc_start: 0.8693 (t0) cc_final: 0.8169 (t0) REVERT: H 60 TYR cc_start: 0.8914 (m-80) cc_final: 0.8647 (m-10) REVERT: L 19 THR cc_start: 0.7420 (m) cc_final: 0.6814 (p) REVERT: L 107 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8018 (mtpp) outliers start: 43 outliers final: 26 residues processed: 187 average time/residue: 0.0934 time to fit residues: 24.8142 Evaluate side-chains 149 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 487 ASN Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN L 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148768 restraints weight = 27589.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149302 restraints weight = 35977.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149365 restraints weight = 33040.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149506 restraints weight = 27702.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150083 restraints weight = 25710.797| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9949 Z= 0.220 Angle : 0.729 12.702 13555 Z= 0.368 Chirality : 0.048 0.256 1470 Planarity : 0.004 0.044 1744 Dihedral : 4.930 62.515 1415 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.37 % Allowed : 20.34 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.24), residues: 1223 helix: 0.54 (0.26), residues: 406 sheet: 0.08 (0.37), residues: 186 loop : -1.13 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 357 TYR 0.023 0.002 TYR A 279 PHE 0.019 0.002 PHE E 497 TRP 0.014 0.002 TRP H 165 HIS 0.007 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 9931) covalent geometry : angle 0.71736 (13519) SS BOND : bond 0.00388 ( 12) SS BOND : angle 2.48973 ( 24) hydrogen bonds : bond 0.04195 ( 378) hydrogen bonds : angle 4.69962 ( 1071) metal coordination : bond 0.00231 ( 2) link_NAG-ASN : bond 0.00745 ( 4) link_NAG-ASN : angle 2.83160 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.5242 (ppp) cc_final: 0.4917 (ttt) REVERT: A 329 GLU cc_start: 0.6979 (pp20) cc_final: 0.6759 (tm-30) REVERT: A 330 ASN cc_start: 0.8102 (m-40) cc_final: 0.7304 (m-40) REVERT: A 350 ASP cc_start: 0.7360 (t0) cc_final: 0.6993 (p0) REVERT: A 366 MET cc_start: 0.7098 (tpp) cc_final: 0.6634 (mmm) REVERT: A 434 THR cc_start: 0.7660 (p) cc_final: 0.7352 (t) REVERT: A 435 GLU cc_start: 0.6996 (pm20) cc_final: 0.6649 (pm20) REVERT: A 479 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: E 406 GLU cc_start: 0.8779 (mp0) cc_final: 0.7661 (mp0) REVERT: E 454 ARG cc_start: 0.8827 (ttm-80) cc_final: 0.8599 (ttm-80) REVERT: E 467 ASP cc_start: 0.8406 (t0) cc_final: 0.7997 (t0) REVERT: H 29 PHE cc_start: 0.6926 (t80) cc_final: 0.6637 (t80) REVERT: H 46 GLU cc_start: 0.8190 (pt0) cc_final: 0.7974 (pt0) REVERT: H 60 TYR cc_start: 0.9039 (m-80) cc_final: 0.8758 (m-10) REVERT: H 87 ARG cc_start: 0.7185 (mpp80) cc_final: 0.6322 (mtt90) REVERT: L 107 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8188 (mtpp) outliers start: 45 outliers final: 29 residues processed: 176 average time/residue: 0.0876 time to fit residues: 22.3265 Evaluate side-chains 152 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 115 optimal weight: 0.0370 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 118 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156532 restraints weight = 25959.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155700 restraints weight = 53028.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156177 restraints weight = 32857.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156322 restraints weight = 25039.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156329 restraints weight = 23383.540| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9949 Z= 0.114 Angle : 0.603 8.662 13555 Z= 0.301 Chirality : 0.043 0.161 1470 Planarity : 0.003 0.038 1744 Dihedral : 4.684 76.691 1415 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.95 % Allowed : 22.15 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1223 helix: 0.77 (0.26), residues: 409 sheet: 0.29 (0.37), residues: 184 loop : -1.01 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 357 TYR 0.015 0.001 TYR A 279 PHE 0.020 0.001 PHE A 555 TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9931) covalent geometry : angle 0.59435 (13519) SS BOND : bond 0.00385 ( 12) SS BOND : angle 1.88810 ( 24) hydrogen bonds : bond 0.03567 ( 378) hydrogen bonds : angle 4.43928 ( 1071) metal coordination : bond 0.00070 ( 2) link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 2.35758 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.5022 (ppp) cc_final: 0.4617 (ttt) REVERT: A 350 ASP cc_start: 0.7293 (t0) cc_final: 0.6954 (p0) REVERT: A 434 THR cc_start: 0.7880 (p) cc_final: 0.7283 (t) REVERT: A 435 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: A 479 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: E 406 GLU cc_start: 0.8601 (mp0) cc_final: 0.7701 (mp0) REVERT: E 467 ASP cc_start: 0.8448 (t0) cc_final: 0.7956 (t0) REVERT: H 60 TYR cc_start: 0.8939 (m-80) cc_final: 0.8707 (m-10) REVERT: L 64 PHE cc_start: 0.7827 (m-80) cc_final: 0.7598 (m-80) REVERT: L 107 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8126 (mtpp) outliers start: 30 outliers final: 20 residues processed: 159 average time/residue: 0.0895 time to fit residues: 20.3388 Evaluate side-chains 147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 40 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS A 401 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.159183 restraints weight = 21546.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148029 restraints weight = 39311.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145230 restraints weight = 33157.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144742 restraints weight = 34716.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145272 restraints weight = 28179.300| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9949 Z= 0.194 Angle : 0.690 8.425 13555 Z= 0.346 Chirality : 0.046 0.157 1470 Planarity : 0.004 0.037 1744 Dihedral : 5.054 83.060 1415 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.61 % Allowed : 22.34 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1223 helix: 0.57 (0.26), residues: 411 sheet: 0.07 (0.37), residues: 183 loop : -1.00 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.021 0.002 TYR H 205 PHE 0.023 0.002 PHE H 64 TRP 0.015 0.002 TRP H 165 HIS 0.008 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9931) covalent geometry : angle 0.68353 (13519) SS BOND : bond 0.00388 ( 12) SS BOND : angle 1.80995 ( 24) hydrogen bonds : bond 0.04122 ( 378) hydrogen bonds : angle 4.60804 ( 1071) metal coordination : bond 0.00097 ( 2) link_NAG-ASN : bond 0.00329 ( 4) link_NAG-ASN : angle 2.22205 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASN cc_start: 0.7697 (m-40) cc_final: 0.7021 (t0) REVERT: A 279 TYR cc_start: 0.7605 (t80) cc_final: 0.7133 (t80) REVERT: A 434 THR cc_start: 0.8477 (p) cc_final: 0.8096 (t) REVERT: A 435 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6778 (pm20) REVERT: A 479 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: A 526 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8317 (tp40) REVERT: E 406 GLU cc_start: 0.8667 (mp0) cc_final: 0.7714 (mp0) REVERT: E 467 ASP cc_start: 0.8589 (t0) cc_final: 0.8239 (t0) REVERT: H 29 PHE cc_start: 0.6986 (t80) cc_final: 0.6713 (t80) REVERT: H 60 TYR cc_start: 0.9096 (m-80) cc_final: 0.8821 (m-10) REVERT: H 165 TRP cc_start: 0.0418 (OUTLIER) cc_final: 0.0167 (t-100) REVERT: L 107 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8144 (mtpp) outliers start: 37 outliers final: 31 residues processed: 155 average time/residue: 0.0889 time to fit residues: 19.7906 Evaluate side-chains 156 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 165 TRP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153522 restraints weight = 25915.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151268 restraints weight = 57350.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151315 restraints weight = 36777.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151003 restraints weight = 26120.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151187 restraints weight = 24038.328| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9949 Z= 0.144 Angle : 0.650 11.304 13555 Z= 0.325 Chirality : 0.045 0.228 1470 Planarity : 0.003 0.032 1744 Dihedral : 4.747 71.942 1415 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.33 % Allowed : 23.29 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1223 helix: 0.61 (0.26), residues: 412 sheet: 0.02 (0.37), residues: 183 loop : -0.95 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 357 TYR 0.013 0.001 TYR H 205 PHE 0.021 0.002 PHE A 555 TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9931) covalent geometry : angle 0.64469 (13519) SS BOND : bond 0.00362 ( 12) SS BOND : angle 1.63598 ( 24) hydrogen bonds : bond 0.03780 ( 378) hydrogen bonds : angle 4.59809 ( 1071) metal coordination : bond 0.00083 ( 2) link_NAG-ASN : bond 0.00388 ( 4) link_NAG-ASN : angle 2.02802 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASN cc_start: 0.7483 (m-40) cc_final: 0.6879 (t0) REVERT: A 279 TYR cc_start: 0.7700 (t80) cc_final: 0.7413 (t80) REVERT: A 434 THR cc_start: 0.8396 (p) cc_final: 0.8049 (t) REVERT: A 435 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6819 (pm20) REVERT: A 479 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: A 526 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: E 406 GLU cc_start: 0.8562 (mp0) cc_final: 0.7665 (mp0) REVERT: E 467 ASP cc_start: 0.8298 (t0) cc_final: 0.7850 (t0) REVERT: H 29 PHE cc_start: 0.7018 (t80) cc_final: 0.6691 (t80) REVERT: H 60 TYR cc_start: 0.9066 (m-80) cc_final: 0.8805 (m-10) REVERT: H 165 TRP cc_start: 0.0160 (OUTLIER) cc_final: -0.0113 (t-100) REVERT: L 87 ASP cc_start: 0.7658 (p0) cc_final: 0.7432 (p0) REVERT: L 107 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8128 (mtpp) outliers start: 34 outliers final: 27 residues processed: 146 average time/residue: 0.0943 time to fit residues: 19.7215 Evaluate side-chains 147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 165 TRP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 72 optimal weight: 0.0970 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 91 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.160810 restraints weight = 15010.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146888 restraints weight = 26460.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145423 restraints weight = 28259.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145134 restraints weight = 31047.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145285 restraints weight = 25736.001| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.6669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9949 Z= 0.135 Angle : 0.640 10.742 13555 Z= 0.318 Chirality : 0.044 0.191 1470 Planarity : 0.003 0.031 1744 Dihedral : 4.568 62.808 1415 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.33 % Allowed : 23.10 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1223 helix: 0.63 (0.26), residues: 419 sheet: 0.05 (0.37), residues: 183 loop : -0.93 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 357 TYR 0.011 0.001 TYR H 205 PHE 0.021 0.002 PHE H 64 TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9931) covalent geometry : angle 0.63552 (13519) SS BOND : bond 0.00350 ( 12) SS BOND : angle 1.51071 ( 24) hydrogen bonds : bond 0.03733 ( 378) hydrogen bonds : angle 4.54930 ( 1071) metal coordination : bond 0.00039 ( 2) link_NAG-ASN : bond 0.00397 ( 4) link_NAG-ASN : angle 1.88737 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASN cc_start: 0.7609 (m-40) cc_final: 0.6922 (t0) REVERT: A 279 TYR cc_start: 0.7736 (t80) cc_final: 0.7407 (t80) REVERT: A 323 MET cc_start: 0.9114 (mmm) cc_final: 0.8752 (mmp) REVERT: A 434 THR cc_start: 0.8449 (p) cc_final: 0.8097 (t) REVERT: A 435 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: A 479 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: A 526 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7998 (tp40) REVERT: E 406 GLU cc_start: 0.8548 (mp0) cc_final: 0.7679 (mp0) REVERT: E 467 ASP cc_start: 0.8177 (t0) cc_final: 0.7927 (t0) REVERT: H 29 PHE cc_start: 0.7028 (t80) cc_final: 0.6714 (t80) REVERT: H 60 TYR cc_start: 0.9064 (m-80) cc_final: 0.8793 (m-10) REVERT: H 165 TRP cc_start: 0.0404 (OUTLIER) cc_final: 0.0092 (t-100) REVERT: L 87 ASP cc_start: 0.7633 (p0) cc_final: 0.7412 (p0) REVERT: L 107 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8095 (mtpp) outliers start: 34 outliers final: 25 residues processed: 147 average time/residue: 0.0865 time to fit residues: 18.5782 Evaluate side-chains 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 165 TRP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.168690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148799 restraints weight = 19503.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147583 restraints weight = 26829.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148199 restraints weight = 25800.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148153 restraints weight = 20072.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148215 restraints weight = 20463.649| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9949 Z= 0.124 Angle : 0.644 9.280 13555 Z= 0.320 Chirality : 0.044 0.202 1470 Planarity : 0.003 0.030 1744 Dihedral : 4.281 48.120 1415 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.33 % Allowed : 23.48 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1223 helix: 0.66 (0.26), residues: 419 sheet: 0.25 (0.38), residues: 185 loop : -0.93 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 357 TYR 0.010 0.001 TYR A 41 PHE 0.020 0.002 PHE H 64 TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9931) covalent geometry : angle 0.63380 (13519) SS BOND : bond 0.00366 ( 12) SS BOND : angle 2.48280 ( 24) hydrogen bonds : bond 0.03683 ( 378) hydrogen bonds : angle 4.47997 ( 1071) metal coordination : bond 0.00059 ( 2) link_NAG-ASN : bond 0.00415 ( 4) link_NAG-ASN : angle 1.80371 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASN cc_start: 0.7589 (m-40) cc_final: 0.6821 (t0) REVERT: A 257 SER cc_start: 0.4468 (t) cc_final: 0.3838 (p) REVERT: A 279 TYR cc_start: 0.7613 (t80) cc_final: 0.7237 (t80) REVERT: A 323 MET cc_start: 0.9102 (mmm) cc_final: 0.8788 (mmp) REVERT: A 373 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8464 (m170) REVERT: A 434 THR cc_start: 0.8425 (p) cc_final: 0.8099 (t) REVERT: A 435 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: A 479 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: A 526 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8014 (tp40) REVERT: A 582 ARG cc_start: 0.7591 (tpm170) cc_final: 0.7372 (tpm170) REVERT: E 406 GLU cc_start: 0.8552 (mp0) cc_final: 0.7680 (mp0) REVERT: E 467 ASP cc_start: 0.8189 (t0) cc_final: 0.7653 (t0) REVERT: H 29 PHE cc_start: 0.6977 (t80) cc_final: 0.6671 (t80) REVERT: H 60 TYR cc_start: 0.8968 (m-80) cc_final: 0.8750 (m-10) REVERT: L 87 ASP cc_start: 0.7755 (p0) cc_final: 0.7519 (p0) outliers start: 34 outliers final: 25 residues processed: 152 average time/residue: 0.0853 time to fit residues: 18.9118 Evaluate side-chains 149 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.0010 chunk 3 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.168612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153226 restraints weight = 29330.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151712 restraints weight = 58974.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152161 restraints weight = 40496.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152516 restraints weight = 25018.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152441 restraints weight = 22719.099| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 9949 Z= 0.251 Angle : 0.926 59.200 13555 Z= 0.536 Chirality : 0.044 0.284 1470 Planarity : 0.004 0.057 1744 Dihedral : 4.468 50.118 1415 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 3.23 % Allowed : 23.57 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1223 helix: 0.66 (0.26), residues: 419 sheet: 0.25 (0.38), residues: 185 loop : -0.94 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.010 0.001 TYR A 41 PHE 0.018 0.001 PHE H 64 TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9931) covalent geometry : angle 0.91935 (13519) SS BOND : bond 0.00409 ( 12) SS BOND : angle 2.46835 ( 24) hydrogen bonds : bond 0.03676 ( 378) hydrogen bonds : angle 4.47924 ( 1071) metal coordination : bond 0.00057 ( 2) link_NAG-ASN : bond 0.00418 ( 4) link_NAG-ASN : angle 1.79465 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1622.48 seconds wall clock time: 28 minutes 48.90 seconds (1728.90 seconds total)