Starting phenix.real_space_refine on Thu Mar 5 23:14:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xw6_33492/03_2026/7xw6_33492_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xw6_33492/03_2026/7xw6_33492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xw6_33492/03_2026/7xw6_33492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xw6_33492/03_2026/7xw6_33492.map" model { file = "/net/cci-nas-00/data/ceres_data/7xw6_33492/03_2026/7xw6_33492_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xw6_33492/03_2026/7xw6_33492_neut_trim.cif" } resolution = 2.78 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 8370 2.51 5 N 2099 2.21 5 O 2337 1.98 5 H 12117 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24998 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3879 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5107 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "L" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1648 Classifications: {'peptide': 112} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 105} Chain: "N" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1911 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 9053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9053 Classifications: {'peptide': 562} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 535} Chain breaks: 2 Chain: "Y" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1854 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "R" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 661 Unusual residues: {'CLR': 17, 'HOI': 1, 'NAG': 4, 'PLM': 5} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.57, per 1000 atoms: 0.18 Number of scatterers: 24998 At special positions: 0 Unit cell: (83.224, 103, 191.992, 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) S 75 16.00 O 2337 8.00 N 2099 7.00 C 8370 6.00 H 12117 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 41 " distance=2.05 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.01 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.01 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.04 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 R 801 " - " ASN R 198 " " NAG R 802 " - " ASN R 177 " " NAG R 803 " - " ASN R 99 " " NAG R 804 " - " ASN R 77 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 792.9 milliseconds 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2916 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 20 sheets defined 31.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 4.148A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.533A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.736A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.515A pdb=" N GLU A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.976A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 4 through 26 removed outlier: 4.446A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.552A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.523A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.607A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.687A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 265 through 270 removed outlier: 4.017A pdb=" N LEU R 270 " --> pdb=" O LEU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 290 removed outlier: 4.655A pdb=" N ASN R 288 " --> pdb=" O ALA R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 430 removed outlier: 4.554A pdb=" N TRP R 422 " --> pdb=" O ARG R 418 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE R 423 " --> pdb=" O ILE R 419 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 442 Processing helix chain 'R' and resid 447 through 478 Processing helix chain 'R' and resid 480 through 483 Processing helix chain 'R' and resid 484 through 491 Processing helix chain 'R' and resid 491 through 525 removed outlier: 3.728A pdb=" N ASN R 495 " --> pdb=" O GLY R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 528 through 532 removed outlier: 3.663A pdb=" N LYS R 532 " --> pdb=" O LEU R 529 " (cutoff:3.500A) Processing helix chain 'R' and resid 534 through 559 Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 576 through 609 Processing helix chain 'R' and resid 618 through 649 removed outlier: 3.593A pdb=" N ALA R 623 " --> pdb=" O ASP R 619 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU R 629 " --> pdb=" O ARG R 625 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 658 through 666 removed outlier: 4.100A pdb=" N LEU R 662 " --> pdb=" O ASN R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 668 through 679 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 682 through 694 Processing helix chain 'Y' and resid 28 through 32 removed outlier: 3.628A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.175A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.465A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.568A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.805A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.633A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.273A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.813A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.753A pdb=" N GLY L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.753A pdb=" N GLY L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.998A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 29 through 33 removed outlier: 7.398A pdb=" N PHE R 37 " --> pdb=" O GLN R 55 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU R 57 " --> pdb=" O PHE R 37 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL R 39 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU R 59 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS R 41 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU R 61 " --> pdb=" O CYS R 41 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU R 61 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP R 86 " --> pdb=" O GLU R 61 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE R 81 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG R 109 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL R 83 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR R 111 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE R 85 " --> pdb=" O THR R 111 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR R 136 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASN R 110 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU R 180 " --> pdb=" O ALA R 204 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N TYR R 206 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU R 182 " --> pdb=" O TYR R 206 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N LEU R 230 " --> pdb=" O LYS R 201 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASP R 203 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.760A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'R' and resid 166 through 167 Processing sheet with id=AB9, first strand: chain 'Y' and resid 3 through 6 removed outlier: 3.776A pdb=" N GLN Y 3 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.038A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 10 through 12 removed outlier: 4.432A pdb=" N ASN Y 102 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1482 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: 6.07 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 2777 1.02 - 1.22: 9416 1.22 - 1.42: 5377 1.42 - 1.62: 7638 1.62 - 1.82: 103 Bond restraints: 25311 Sorted by residual: bond pdb=" CD1 PHE R 269 " pdb=" HD1 PHE R 269 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CE3 TRP R 546 " pdb=" HE3 TRP R 546 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN A 367 " pdb=" H ASN A 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 HIS B 91 " pdb=" HD2 HIS B 91 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG A 332 " pdb="HH11 ARG A 332 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 25306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.42: 44724 6.42 - 12.84: 642 12.84 - 19.26: 4 19.26 - 25.67: 1 25.67 - 32.09: 2 Bond angle restraints: 45373 Sorted by residual: angle pdb=" N TYR R 225 " pdb=" CA TYR R 225 " pdb=" HA TYR R 225 " ideal model delta sigma weight residual 110.00 77.91 32.09 3.00e+00 1.11e-01 1.14e+02 angle pdb=" N TYR R 225 " pdb=" CA TYR R 225 " pdb=" C TYR R 225 " ideal model delta sigma weight residual 111.71 123.68 -11.97 1.15e+00 7.56e-01 1.08e+02 angle pdb=" C TYR R 225 " pdb=" CA TYR R 225 " pdb=" HA TYR R 225 " ideal model delta sigma weight residual 109.00 82.37 26.63 3.00e+00 1.11e-01 7.88e+01 angle pdb=" CB TYR R 225 " pdb=" CA TYR R 225 " pdb=" HA TYR R 225 " ideal model delta sigma weight residual 109.00 83.93 25.07 3.00e+00 1.11e-01 6.98e+01 angle pdb=" CA PHE N 68 " pdb=" CB PHE N 68 " pdb=" CG PHE N 68 " ideal model delta sigma weight residual 113.80 120.02 -6.22 1.00e+00 1.00e+00 3.87e+01 ... (remaining 45368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 12277 23.94 - 47.87: 441 47.87 - 71.81: 184 71.81 - 95.75: 22 95.75 - 119.68: 2 Dihedral angle restraints: 12926 sinusoidal: 7555 harmonic: 5371 Sorted by residual: dihedral pdb=" N TYR R 225 " pdb=" C TYR R 225 " pdb=" CA TYR R 225 " pdb=" CB TYR R 225 " ideal model delta harmonic sigma weight residual 122.80 149.88 -27.08 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" C TYR R 225 " pdb=" N TYR R 225 " pdb=" CA TYR R 225 " pdb=" CB TYR R 225 " ideal model delta harmonic sigma weight residual -122.60 -149.16 26.56 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" C LEU A 256 " pdb=" N LEU A 256 " pdb=" CA LEU A 256 " pdb=" CB LEU A 256 " ideal model delta harmonic sigma weight residual -122.60 -138.08 15.48 0 2.50e+00 1.60e-01 3.83e+01 ... (remaining 12923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 2008 0.235 - 0.470: 60 0.470 - 0.704: 3 0.704 - 0.939: 0 0.939 - 1.174: 1 Chirality restraints: 2072 Sorted by residual: chirality pdb=" CA TYR R 225 " pdb=" N TYR R 225 " pdb=" C TYR R 225 " pdb=" CB TYR R 225 " both_signs ideal model delta sigma weight residual False 2.51 1.34 1.17 2.00e-01 2.50e+01 3.45e+01 chirality pdb=" CA LEU A 256 " pdb=" N LEU A 256 " pdb=" C LEU A 256 " pdb=" CB LEU A 256 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CA LEU R 207 " pdb=" N LEU R 207 " pdb=" C LEU R 207 " pdb=" CB LEU R 207 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 2069 not shown) Planarity restraints: 3656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HOI R 827 " 0.096 2.00e-02 2.50e+03 1.71e-01 6.61e+02 pdb=" C11 HOI R 827 " 0.010 2.00e-02 2.50e+03 pdb=" C12 HOI R 827 " 0.114 2.00e-02 2.50e+03 pdb=" C13 HOI R 827 " 0.201 2.00e-02 2.50e+03 pdb=" C14 HOI R 827 " 0.062 2.00e-02 2.50e+03 pdb=" C15 HOI R 827 " 0.054 2.00e-02 2.50e+03 pdb=" C16 HOI R 827 " -0.296 2.00e-02 2.50e+03 pdb=" C9 HOI R 827 " 0.079 2.00e-02 2.50e+03 pdb=" O5 HOI R 827 " -0.318 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 99 " -0.213 2.00e-02 2.50e+03 1.59e-01 3.81e+02 pdb=" CG ASN R 99 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN R 99 " 0.107 2.00e-02 2.50e+03 pdb=" ND2 ASN R 99 " 0.122 2.00e-02 2.50e+03 pdb="HD21 ASN R 99 " 0.148 2.00e-02 2.50e+03 pdb=" C1 NAG R 803 " -0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 77 " -0.190 2.00e-02 2.50e+03 1.56e-01 3.67e+02 pdb=" CG ASN R 77 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN R 77 " 0.153 2.00e-02 2.50e+03 pdb=" ND2 ASN R 77 " -0.035 2.00e-02 2.50e+03 pdb="HD21 ASN R 77 " 0.222 2.00e-02 2.50e+03 pdb=" C1 NAG R 804 " -0.188 2.00e-02 2.50e+03 ... (remaining 3653 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1586 2.18 - 2.79: 42760 2.79 - 3.39: 69341 3.39 - 4.00: 94120 4.00 - 4.60: 136604 Nonbonded interactions: 344411 Sorted by model distance: nonbonded pdb=" HG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP R 143 " pdb=" HG1 THR R 145 " model vdw 1.589 2.450 nonbonded pdb=" OD1 ASP Y 72 " pdb=" HG SER Y 74 " model vdw 1.601 2.450 nonbonded pdb=" HG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP A 249 " pdb=" HG SER A 251 " model vdw 1.610 2.450 ... (remaining 344406 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.013 0.075 13206 Z= 0.764 Angle : 1.795 11.972 17995 Z= 1.176 Chirality : 0.108 1.174 2072 Planarity : 0.015 0.171 2169 Dihedral : 12.297 119.682 5817 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.07 % Allowed : 0.59 % Favored : 99.33 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 3.51 % 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: -0.16 (0.21), residues: 1530 helix: -0.07 (0.24), residues: 385 sheet: 0.67 (0.28), residues: 323 loop : -0.37 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 48 TYR 0.111 0.018 TYR Y 56 PHE 0.064 0.014 PHE A 222 TRP 0.119 0.022 TRP R 488 HIS 0.013 0.004 HIS R 282 Details of bonding type rmsd covalent geometry : bond 0.01326 (13194) covalent geometry : angle 1.79004 (17967) SS BOND : bond 0.01315 ( 8) SS BOND : angle 2.60241 ( 16) hydrogen bonds : bond 0.17048 ( 539) hydrogen bonds : angle 7.18359 ( 1482) link_NAG-ASN : bond 0.01426 ( 4) link_NAG-ASN : angle 4.75340 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.7339 (mmm) cc_final: 0.7051 (mtp) REVERT: A 334 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7125 (mm-30) REVERT: B 155 ASN cc_start: 0.7666 (t0) cc_final: 0.7086 (t0) REVERT: B 218 CYS cc_start: 0.7690 (p) cc_final: 0.7428 (p) REVERT: G 17 GLU cc_start: 0.7831 (tp30) cc_final: 0.7608 (tp30) REVERT: G 24 ASN cc_start: 0.7492 (m-40) cc_final: 0.6946 (m-40) REVERT: R 239 THR cc_start: 0.8355 (p) cc_final: 0.8144 (m) REVERT: R 465 MET cc_start: 0.7774 (tpt) cc_final: 0.7499 (tpt) REVERT: R 642 PHE cc_start: 0.8138 (t80) cc_final: 0.7926 (t80) REVERT: R 658 ASN cc_start: 0.8600 (m-40) cc_final: 0.8351 (m-40) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 1.2073 time to fit residues: 500.4028 Evaluate side-chains 326 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 88 ASN B 125 ASN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Y 66 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.157086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127058 restraints weight = 50438.158| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.26 r_work: 0.3555 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13206 Z= 0.172 Angle : 0.672 8.267 17995 Z= 0.356 Chirality : 0.044 0.379 2072 Planarity : 0.005 0.049 2169 Dihedral : 7.253 76.590 2974 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.85 % Allowed : 9.19 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.27 (0.21), residues: 1530 helix: 1.29 (0.26), residues: 392 sheet: 0.12 (0.26), residues: 368 loop : -0.30 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 625 TYR 0.018 0.002 TYR R 667 PHE 0.023 0.002 PHE N 29 TRP 0.024 0.002 TRP B 82 HIS 0.008 0.002 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00388 (13194) covalent geometry : angle 0.66004 (17967) SS BOND : bond 0.01091 ( 8) SS BOND : angle 2.93234 ( 16) hydrogen bonds : bond 0.05371 ( 539) hydrogen bonds : angle 5.55505 ( 1482) link_NAG-ASN : bond 0.00679 ( 4) link_NAG-ASN : angle 3.66442 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 341 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7740 (mp10) REVERT: A 60 MET cc_start: 0.7675 (mmm) cc_final: 0.7415 (mtp) REVERT: A 371 ASP cc_start: 0.8345 (t70) cc_final: 0.7994 (t0) REVERT: B 99 TRP cc_start: 0.8142 (m-90) cc_final: 0.7455 (m-90) REVERT: G 17 GLU cc_start: 0.8093 (tp30) cc_final: 0.7869 (tp30) REVERT: G 24 ASN cc_start: 0.7673 (m-40) cc_final: 0.7201 (m-40) REVERT: L 35 TRP cc_start: 0.7871 (m100) cc_final: 0.7100 (m100) REVERT: N 21 SER cc_start: 0.8242 (t) cc_final: 0.7966 (p) REVERT: N 31 ASN cc_start: 0.8309 (m110) cc_final: 0.7990 (m110) REVERT: N 113 THR cc_start: 0.8837 (t) cc_final: 0.8608 (p) REVERT: R 30 GLU cc_start: 0.6036 (tm-30) cc_final: 0.5793 (tm-30) REVERT: R 123 LYS cc_start: 0.8360 (pttt) cc_final: 0.7978 (pttt) REVERT: R 239 THR cc_start: 0.8689 (p) cc_final: 0.8477 (m) REVERT: R 460 ASP cc_start: 0.8026 (m-30) cc_final: 0.7751 (m-30) REVERT: R 463 MET cc_start: 0.8535 (tpp) cc_final: 0.8311 (tpp) REVERT: R 465 MET cc_start: 0.8275 (tpt) cc_final: 0.7934 (tpt) REVERT: Y 59 TYR cc_start: 0.8228 (m-80) cc_final: 0.7991 (m-80) REVERT: Y 91 TYR cc_start: 0.7240 (m-80) cc_final: 0.6952 (m-80) outliers start: 25 outliers final: 11 residues processed: 348 average time/residue: 1.2691 time to fit residues: 482.9640 Evaluate side-chains 325 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 314 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 426 LEU Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 66 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 48 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 340 ASN G 18 GLN N 120 GLN R 186 ASN Y 66 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125518 restraints weight = 50301.506| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.24 r_work: 0.3525 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13206 Z= 0.189 Angle : 0.610 6.787 17995 Z= 0.323 Chirality : 0.043 0.361 2072 Planarity : 0.004 0.049 2169 Dihedral : 6.642 62.363 2974 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.63 % Allowed : 13.27 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.21), residues: 1530 helix: 1.68 (0.26), residues: 392 sheet: -0.07 (0.26), residues: 389 loop : -0.26 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 270 TYR 0.015 0.002 TYR L 49 PHE 0.017 0.002 PHE B 235 TRP 0.020 0.002 TRP N 47 HIS 0.013 0.002 HIS Y 66 Details of bonding type rmsd covalent geometry : bond 0.00436 (13194) covalent geometry : angle 0.60167 (17967) SS BOND : bond 0.00528 ( 8) SS BOND : angle 2.09033 ( 16) hydrogen bonds : bond 0.04960 ( 539) hydrogen bonds : angle 5.17948 ( 1482) link_NAG-ASN : bond 0.00461 ( 4) link_NAG-ASN : angle 3.10365 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7788 (mp10) REVERT: A 60 MET cc_start: 0.7771 (mmm) cc_final: 0.7566 (mtp) REVERT: A 324 VAL cc_start: 0.8087 (p) cc_final: 0.7656 (m) REVERT: A 371 ASP cc_start: 0.8384 (t70) cc_final: 0.8045 (t0) REVERT: B 99 TRP cc_start: 0.8261 (m-90) cc_final: 0.7875 (m100) REVERT: B 155 ASN cc_start: 0.8155 (t0) cc_final: 0.7697 (t0) REVERT: B 217 MET cc_start: 0.7127 (mmm) cc_final: 0.6915 (tmm) REVERT: G 17 GLU cc_start: 0.8036 (tp30) cc_final: 0.7827 (tp30) REVERT: G 24 ASN cc_start: 0.7675 (m-40) cc_final: 0.7207 (m-40) REVERT: L 35 TRP cc_start: 0.7976 (m100) cc_final: 0.7309 (m100) REVERT: N 21 SER cc_start: 0.8331 (t) cc_final: 0.7964 (p) REVERT: N 31 ASN cc_start: 0.8302 (m110) cc_final: 0.7993 (m110) REVERT: R 30 GLU cc_start: 0.6019 (tm-30) cc_final: 0.5708 (tm-30) REVERT: R 123 LYS cc_start: 0.8401 (pttt) cc_final: 0.7958 (pttt) REVERT: R 239 THR cc_start: 0.8694 (p) cc_final: 0.8488 (m) REVERT: R 465 MET cc_start: 0.8332 (tpt) cc_final: 0.7972 (tpt) REVERT: Y 36 TRP cc_start: 0.7383 (m100) cc_final: 0.7117 (m100) REVERT: Y 59 TYR cc_start: 0.8191 (m-80) cc_final: 0.7958 (m-80) REVERT: Y 91 TYR cc_start: 0.7247 (m-80) cc_final: 0.6988 (m-80) outliers start: 22 outliers final: 13 residues processed: 339 average time/residue: 1.2993 time to fit residues: 481.3781 Evaluate side-chains 330 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 317 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain R residue 478 HIS Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 129 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.154992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125175 restraints weight = 50306.671| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.24 r_work: 0.3530 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13206 Z= 0.169 Angle : 0.571 5.716 17995 Z= 0.301 Chirality : 0.042 0.356 2072 Planarity : 0.004 0.057 2169 Dihedral : 6.394 60.171 2974 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.11 % Allowed : 15.05 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.22), residues: 1530 helix: 1.89 (0.27), residues: 392 sheet: -0.12 (0.26), residues: 389 loop : -0.30 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 76 TYR 0.013 0.001 TYR R 582 PHE 0.014 0.001 PHE R 416 TRP 0.019 0.002 TRP N 47 HIS 0.009 0.001 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00385 (13194) covalent geometry : angle 0.56402 (17967) SS BOND : bond 0.00347 ( 8) SS BOND : angle 1.83835 ( 16) hydrogen bonds : bond 0.04598 ( 539) hydrogen bonds : angle 4.99681 ( 1482) link_NAG-ASN : bond 0.00394 ( 4) link_NAG-ASN : angle 2.82566 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 329 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7807 (mp10) REVERT: A 256 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6707 (tt) REVERT: A 324 VAL cc_start: 0.8001 (p) cc_final: 0.7594 (m) REVERT: A 371 ASP cc_start: 0.8357 (t70) cc_final: 0.8054 (t0) REVERT: B 76 ASP cc_start: 0.8233 (p0) cc_final: 0.8032 (p0) REVERT: B 155 ASN cc_start: 0.8141 (t0) cc_final: 0.7687 (t0) REVERT: G 17 GLU cc_start: 0.8032 (tp30) cc_final: 0.7761 (tp30) REVERT: G 24 ASN cc_start: 0.7683 (m-40) cc_final: 0.7230 (m-40) REVERT: L 35 TRP cc_start: 0.7927 (m100) cc_final: 0.7207 (m100) REVERT: N 21 SER cc_start: 0.8305 (t) cc_final: 0.7908 (p) REVERT: N 31 ASN cc_start: 0.8303 (m110) cc_final: 0.7986 (m110) REVERT: R 30 GLU cc_start: 0.6112 (tm-30) cc_final: 0.5790 (tm-30) REVERT: R 83 VAL cc_start: 0.7887 (t) cc_final: 0.7666 (t) REVERT: R 123 LYS cc_start: 0.8424 (pttt) cc_final: 0.7981 (pttt) REVERT: R 239 THR cc_start: 0.8686 (p) cc_final: 0.8469 (m) REVERT: R 463 MET cc_start: 0.8415 (tpp) cc_final: 0.8011 (tpp) REVERT: R 465 MET cc_start: 0.8323 (tpt) cc_final: 0.7960 (tpt) REVERT: Y 36 TRP cc_start: 0.7343 (m100) cc_final: 0.7043 (m100) REVERT: Y 59 TYR cc_start: 0.8221 (m-80) cc_final: 0.8009 (m-80) REVERT: Y 66 HIS cc_start: 0.7080 (m170) cc_final: 0.6832 (m170) REVERT: Y 91 TYR cc_start: 0.7268 (m-80) cc_final: 0.6976 (m-80) outliers start: 15 outliers final: 10 residues processed: 338 average time/residue: 1.1952 time to fit residues: 443.0699 Evaluate side-chains 330 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 319 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 1.9990 chunk 115 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.154707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124999 restraints weight = 50335.370| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.23 r_work: 0.3523 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13206 Z= 0.156 Angle : 0.551 5.965 17995 Z= 0.288 Chirality : 0.041 0.359 2072 Planarity : 0.004 0.062 2169 Dihedral : 6.162 56.668 2974 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.78 % Allowed : 15.27 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.22), residues: 1530 helix: 2.02 (0.27), residues: 385 sheet: -0.20 (0.26), residues: 391 loop : -0.25 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 76 TYR 0.015 0.001 TYR R 482 PHE 0.021 0.001 PHE R 134 TRP 0.019 0.002 TRP N 47 HIS 0.008 0.001 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00358 (13194) covalent geometry : angle 0.54472 (17967) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.84257 ( 16) hydrogen bonds : bond 0.04350 ( 539) hydrogen bonds : angle 4.84329 ( 1482) link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 2.57799 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7850 (mp10) REVERT: A 256 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6752 (tp) REVERT: A 371 ASP cc_start: 0.8367 (t70) cc_final: 0.8071 (t0) REVERT: B 217 MET cc_start: 0.7208 (mmm) cc_final: 0.6919 (mmm) REVERT: G 17 GLU cc_start: 0.7974 (tp30) cc_final: 0.7680 (tp30) REVERT: G 24 ASN cc_start: 0.7697 (m-40) cc_final: 0.7264 (m-40) REVERT: L 35 TRP cc_start: 0.7912 (m100) cc_final: 0.7268 (m100) REVERT: N 21 SER cc_start: 0.8247 (t) cc_final: 0.7850 (p) REVERT: N 31 ASN cc_start: 0.8293 (m110) cc_final: 0.8017 (m110) REVERT: R 30 GLU cc_start: 0.6135 (tm-30) cc_final: 0.5828 (tm-30) REVERT: R 83 VAL cc_start: 0.7836 (t) cc_final: 0.7618 (t) REVERT: R 123 LYS cc_start: 0.8447 (pttt) cc_final: 0.8015 (pttt) REVERT: R 239 THR cc_start: 0.8680 (p) cc_final: 0.8466 (m) REVERT: R 420 VAL cc_start: 0.8680 (p) cc_final: 0.8390 (t) REVERT: R 463 MET cc_start: 0.8413 (tpp) cc_final: 0.7986 (tpp) REVERT: R 465 MET cc_start: 0.8306 (tpt) cc_final: 0.7933 (tpt) REVERT: R 528 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7868 (mmm160) REVERT: Y 36 TRP cc_start: 0.7347 (m100) cc_final: 0.7121 (m100) REVERT: Y 66 HIS cc_start: 0.7181 (m170) cc_final: 0.6941 (m170) REVERT: Y 91 TYR cc_start: 0.7275 (m-80) cc_final: 0.6984 (m-80) outliers start: 24 outliers final: 13 residues processed: 337 average time/residue: 1.1831 time to fit residues: 437.9644 Evaluate side-chains 324 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 310 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.153375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123488 restraints weight = 50058.985| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.24 r_work: 0.3504 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13206 Z= 0.211 Angle : 0.572 5.972 17995 Z= 0.300 Chirality : 0.042 0.359 2072 Planarity : 0.004 0.066 2169 Dihedral : 6.182 58.215 2974 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.00 % Allowed : 15.79 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.33 (0.22), residues: 1530 helix: 1.86 (0.27), residues: 388 sheet: -0.21 (0.26), residues: 392 loop : -0.35 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 76 TYR 0.017 0.002 TYR R 482 PHE 0.018 0.002 PHE A 222 TRP 0.020 0.002 TRP N 47 HIS 0.008 0.002 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00487 (13194) covalent geometry : angle 0.56586 (17967) SS BOND : bond 0.00272 ( 8) SS BOND : angle 1.87109 ( 16) hydrogen bonds : bond 0.04608 ( 539) hydrogen bonds : angle 4.82785 ( 1482) link_NAG-ASN : bond 0.00344 ( 4) link_NAG-ASN : angle 2.52643 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 328 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7852 (mp10) REVERT: A 251 SER cc_start: 0.8317 (p) cc_final: 0.8108 (m) REVERT: A 324 VAL cc_start: 0.8033 (p) cc_final: 0.7679 (m) REVERT: A 371 ASP cc_start: 0.8427 (t70) cc_final: 0.8113 (t0) REVERT: B 155 ASN cc_start: 0.8244 (t0) cc_final: 0.7883 (t0) REVERT: B 217 MET cc_start: 0.7341 (mmm) cc_final: 0.7082 (mmm) REVERT: G 17 GLU cc_start: 0.7985 (tp30) cc_final: 0.7683 (tp30) REVERT: G 24 ASN cc_start: 0.7727 (m-40) cc_final: 0.7308 (m-40) REVERT: G 46 LYS cc_start: 0.8357 (ptmm) cc_final: 0.8081 (pttt) REVERT: L 35 TRP cc_start: 0.8004 (m100) cc_final: 0.7391 (m100) REVERT: N 21 SER cc_start: 0.8266 (t) cc_final: 0.7806 (p) REVERT: N 31 ASN cc_start: 0.8328 (m110) cc_final: 0.8030 (m110) REVERT: N 80 TYR cc_start: 0.7773 (m-80) cc_final: 0.6973 (m-80) REVERT: R 30 GLU cc_start: 0.6153 (tm-30) cc_final: 0.5828 (tm-30) REVERT: R 83 VAL cc_start: 0.7941 (t) cc_final: 0.7714 (t) REVERT: R 123 LYS cc_start: 0.8471 (pttt) cc_final: 0.8065 (pttt) REVERT: R 129 LYS cc_start: 0.8219 (pttp) cc_final: 0.7862 (ptpp) REVERT: R 239 THR cc_start: 0.8677 (p) cc_final: 0.8472 (m) REVERT: R 438 ILE cc_start: 0.8160 (mm) cc_final: 0.7904 (mt) REVERT: R 463 MET cc_start: 0.8443 (tpp) cc_final: 0.8168 (tpp) REVERT: R 465 MET cc_start: 0.8357 (tpt) cc_final: 0.7983 (tpt) outliers start: 27 outliers final: 17 residues processed: 345 average time/residue: 1.2024 time to fit residues: 455.4010 Evaluate side-chains 335 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 318 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 680 ILE Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.155151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.125360 restraints weight = 50036.539| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.25 r_work: 0.3532 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13206 Z= 0.108 Angle : 0.527 5.478 17995 Z= 0.274 Chirality : 0.040 0.354 2072 Planarity : 0.004 0.072 2169 Dihedral : 5.872 54.317 2974 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.41 % Allowed : 16.83 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.51 (0.22), residues: 1530 helix: 2.12 (0.27), residues: 388 sheet: -0.24 (0.25), residues: 395 loop : -0.21 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 76 TYR 0.015 0.001 TYR R 482 PHE 0.017 0.001 PHE A 222 TRP 0.031 0.002 TRP Y 36 HIS 0.005 0.001 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00246 (13194) covalent geometry : angle 0.52190 (17967) SS BOND : bond 0.00263 ( 8) SS BOND : angle 1.51697 ( 16) hydrogen bonds : bond 0.03949 ( 539) hydrogen bonds : angle 4.67125 ( 1482) link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 2.29070 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 316 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7817 (mp10) REVERT: A 251 SER cc_start: 0.8323 (p) cc_final: 0.8099 (m) REVERT: A 371 ASP cc_start: 0.8381 (t70) cc_final: 0.8050 (t0) REVERT: B 51 LEU cc_start: 0.8194 (mp) cc_final: 0.7982 (mt) REVERT: B 217 MET cc_start: 0.7119 (mmm) cc_final: 0.6887 (mmm) REVERT: G 17 GLU cc_start: 0.7974 (tp30) cc_final: 0.7672 (tp30) REVERT: L 35 TRP cc_start: 0.7891 (m100) cc_final: 0.7272 (m100) REVERT: N 21 SER cc_start: 0.8245 (t) cc_final: 0.7844 (p) REVERT: N 31 ASN cc_start: 0.8253 (m110) cc_final: 0.7971 (m110) REVERT: R 30 GLU cc_start: 0.6135 (tm-30) cc_final: 0.5842 (tm-30) REVERT: R 83 VAL cc_start: 0.7740 (t) cc_final: 0.7532 (t) REVERT: R 123 LYS cc_start: 0.8444 (pttt) cc_final: 0.8033 (pttt) REVERT: R 239 THR cc_start: 0.8613 (p) cc_final: 0.8382 (m) REVERT: R 420 VAL cc_start: 0.8633 (p) cc_final: 0.8362 (t) REVERT: R 463 MET cc_start: 0.8441 (tpp) cc_final: 0.8011 (tpp) REVERT: R 465 MET cc_start: 0.8326 (tpt) cc_final: 0.7971 (tpt) REVERT: Y 59 TYR cc_start: 0.8235 (m-80) cc_final: 0.8027 (m-80) REVERT: Y 91 TYR cc_start: 0.7234 (m-80) cc_final: 0.6946 (m-80) outliers start: 19 outliers final: 11 residues processed: 326 average time/residue: 1.1421 time to fit residues: 410.8317 Evaluate side-chains 322 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 311 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 282 ASN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.153424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123682 restraints weight = 49934.883| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.24 r_work: 0.3507 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13206 Z= 0.196 Angle : 0.559 5.879 17995 Z= 0.294 Chirality : 0.041 0.362 2072 Planarity : 0.004 0.075 2169 Dihedral : 5.944 57.883 2974 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 1.56 % Allowed : 17.49 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.34 (0.22), residues: 1530 helix: 1.90 (0.27), residues: 395 sheet: -0.25 (0.25), residues: 399 loop : -0.35 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 76 TYR 0.020 0.002 TYR R 482 PHE 0.017 0.002 PHE N 108 TRP 0.019 0.002 TRP Y 36 HIS 0.008 0.001 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00450 (13194) covalent geometry : angle 0.55339 (17967) SS BOND : bond 0.00309 ( 8) SS BOND : angle 1.87371 ( 16) hydrogen bonds : bond 0.04407 ( 539) hydrogen bonds : angle 4.68968 ( 1482) link_NAG-ASN : bond 0.00309 ( 4) link_NAG-ASN : angle 2.25778 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7886 (mp10) REVERT: A 251 SER cc_start: 0.8327 (p) cc_final: 0.8112 (m) REVERT: B 51 LEU cc_start: 0.8198 (mp) cc_final: 0.7993 (mt) REVERT: B 217 MET cc_start: 0.7331 (mmm) cc_final: 0.7072 (mmm) REVERT: B 233 CYS cc_start: 0.8401 (t) cc_final: 0.8129 (t) REVERT: B 239 ASN cc_start: 0.8188 (m-40) cc_final: 0.7940 (m-40) REVERT: G 17 GLU cc_start: 0.7973 (tp30) cc_final: 0.7667 (tp30) REVERT: G 24 ASN cc_start: 0.7731 (m-40) cc_final: 0.7371 (m-40) REVERT: L 35 TRP cc_start: 0.7983 (m100) cc_final: 0.7377 (m100) REVERT: N 21 SER cc_start: 0.8268 (t) cc_final: 0.7801 (p) REVERT: N 31 ASN cc_start: 0.8306 (m110) cc_final: 0.8016 (m110) REVERT: N 80 TYR cc_start: 0.7704 (m-80) cc_final: 0.6914 (m-80) REVERT: R 30 GLU cc_start: 0.6206 (tm-30) cc_final: 0.5903 (tm-30) REVERT: R 83 VAL cc_start: 0.8014 (t) cc_final: 0.7786 (t) REVERT: R 123 LYS cc_start: 0.8467 (pttt) cc_final: 0.8064 (pttt) REVERT: R 207 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7643 (pp) REVERT: R 239 THR cc_start: 0.8604 (p) cc_final: 0.8397 (m) REVERT: R 463 MET cc_start: 0.8462 (tpp) cc_final: 0.8168 (tpp) REVERT: R 465 MET cc_start: 0.8332 (tpt) cc_final: 0.7978 (tpt) REVERT: Y 91 TYR cc_start: 0.7274 (m-80) cc_final: 0.6916 (m-80) outliers start: 21 outliers final: 15 residues processed: 330 average time/residue: 1.2318 time to fit residues: 447.4055 Evaluate side-chains 332 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 0.0270 chunk 143 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.153945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124243 restraints weight = 50106.915| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.25 r_work: 0.3514 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13206 Z= 0.157 Angle : 0.540 5.867 17995 Z= 0.283 Chirality : 0.041 0.358 2072 Planarity : 0.004 0.076 2169 Dihedral : 5.856 57.837 2974 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 1.56 % Allowed : 17.20 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.22), residues: 1530 helix: 1.84 (0.27), residues: 405 sheet: -0.22 (0.25), residues: 399 loop : -0.42 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 76 TYR 0.020 0.001 TYR R 482 PHE 0.019 0.001 PHE A 222 TRP 0.021 0.002 TRP Y 36 HIS 0.007 0.001 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00359 (13194) covalent geometry : angle 0.53584 (17967) SS BOND : bond 0.00244 ( 8) SS BOND : angle 1.53513 ( 16) hydrogen bonds : bond 0.04188 ( 539) hydrogen bonds : angle 4.64243 ( 1482) link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 2.15850 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 314 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7850 (mp10) REVERT: A 60 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6704 (mtp) REVERT: A 251 SER cc_start: 0.8341 (p) cc_final: 0.8115 (m) REVERT: B 51 LEU cc_start: 0.8199 (mp) cc_final: 0.7989 (mt) REVERT: B 217 MET cc_start: 0.7332 (mmm) cc_final: 0.7068 (mmm) REVERT: B 233 CYS cc_start: 0.8385 (t) cc_final: 0.8105 (t) REVERT: B 239 ASN cc_start: 0.8193 (m-40) cc_final: 0.7958 (m-40) REVERT: G 17 GLU cc_start: 0.7970 (tp30) cc_final: 0.7666 (tp30) REVERT: G 24 ASN cc_start: 0.7735 (m-40) cc_final: 0.7379 (m-40) REVERT: L 35 TRP cc_start: 0.7950 (m100) cc_final: 0.7373 (m100) REVERT: N 21 SER cc_start: 0.8244 (t) cc_final: 0.7791 (p) REVERT: N 31 ASN cc_start: 0.8298 (m110) cc_final: 0.8007 (m110) REVERT: N 80 TYR cc_start: 0.7668 (m-80) cc_final: 0.6891 (m-80) REVERT: R 30 GLU cc_start: 0.6188 (tm-30) cc_final: 0.5883 (tm-30) REVERT: R 83 VAL cc_start: 0.7912 (t) cc_final: 0.7586 (t) REVERT: R 123 LYS cc_start: 0.8444 (pttt) cc_final: 0.8041 (pttt) REVERT: R 207 LEU cc_start: 0.7874 (pp) cc_final: 0.7561 (pt) REVERT: R 239 THR cc_start: 0.8601 (p) cc_final: 0.8372 (m) REVERT: R 262 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8291 (mtmm) REVERT: R 420 VAL cc_start: 0.8631 (p) cc_final: 0.8388 (t) REVERT: R 463 MET cc_start: 0.8447 (tpp) cc_final: 0.7944 (tpp) REVERT: R 465 MET cc_start: 0.8312 (tpt) cc_final: 0.7952 (tpt) REVERT: Y 91 TYR cc_start: 0.7287 (m-80) cc_final: 0.6923 (m-80) outliers start: 21 outliers final: 14 residues processed: 328 average time/residue: 1.1727 time to fit residues: 423.6596 Evaluate side-chains 325 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 310 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.153988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124468 restraints weight = 49804.298| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.23 r_work: 0.3515 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13206 Z= 0.154 Angle : 0.539 6.367 17995 Z= 0.282 Chirality : 0.040 0.359 2072 Planarity : 0.004 0.073 2169 Dihedral : 5.783 57.915 2974 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 1.19 % Allowed : 18.01 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.34 (0.22), residues: 1530 helix: 1.87 (0.27), residues: 404 sheet: -0.20 (0.25), residues: 399 loop : -0.41 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 76 TYR 0.021 0.001 TYR R 482 PHE 0.022 0.001 PHE R 434 TRP 0.023 0.002 TRP Y 36 HIS 0.007 0.001 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00355 (13194) covalent geometry : angle 0.53441 (17967) SS BOND : bond 0.00400 ( 8) SS BOND : angle 1.65014 ( 16) hydrogen bonds : bond 0.04151 ( 539) hydrogen bonds : angle 4.59685 ( 1482) link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 2.02443 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 313 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7851 (mp10) REVERT: A 251 SER cc_start: 0.8366 (p) cc_final: 0.8120 (m) REVERT: B 217 MET cc_start: 0.7382 (mmm) cc_final: 0.7108 (mmm) REVERT: B 233 CYS cc_start: 0.8381 (t) cc_final: 0.8104 (t) REVERT: B 239 ASN cc_start: 0.8184 (m-40) cc_final: 0.7945 (m-40) REVERT: G 17 GLU cc_start: 0.7969 (tp30) cc_final: 0.7663 (tp30) REVERT: G 24 ASN cc_start: 0.7756 (m-40) cc_final: 0.7406 (m-40) REVERT: L 35 TRP cc_start: 0.7937 (m100) cc_final: 0.7365 (m100) REVERT: N 21 SER cc_start: 0.8243 (t) cc_final: 0.7790 (p) REVERT: N 31 ASN cc_start: 0.8285 (m110) cc_final: 0.8025 (m110) REVERT: N 80 TYR cc_start: 0.7649 (m-80) cc_final: 0.6828 (m-80) REVERT: R 83 VAL cc_start: 0.7902 (t) cc_final: 0.7569 (t) REVERT: R 123 LYS cc_start: 0.8405 (pttt) cc_final: 0.8059 (pttt) REVERT: R 135 ASN cc_start: 0.8463 (t0) cc_final: 0.8120 (t0) REVERT: R 207 LEU cc_start: 0.7883 (pp) cc_final: 0.7584 (pt) REVERT: R 239 THR cc_start: 0.8589 (p) cc_final: 0.8357 (m) REVERT: R 262 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8305 (mtmm) REVERT: R 463 MET cc_start: 0.8441 (tpp) cc_final: 0.8134 (tpp) REVERT: R 465 MET cc_start: 0.8300 (tpt) cc_final: 0.7938 (tpt) REVERT: Y 91 TYR cc_start: 0.7285 (m-80) cc_final: 0.6944 (m-80) outliers start: 16 outliers final: 14 residues processed: 323 average time/residue: 1.2086 time to fit residues: 430.1032 Evaluate side-chains 326 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 312 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain Y residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 131 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.153031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123848 restraints weight = 50041.407| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.21 r_work: 0.3513 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13206 Z= 0.195 Angle : 0.558 6.409 17995 Z= 0.293 Chirality : 0.041 0.362 2072 Planarity : 0.004 0.071 2169 Dihedral : 5.833 59.700 2974 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 1.41 % Allowed : 17.87 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.27 (0.22), residues: 1530 helix: 1.77 (0.26), residues: 405 sheet: -0.19 (0.25), residues: 399 loop : -0.45 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 76 TYR 0.024 0.001 TYR R 482 PHE 0.022 0.002 PHE R 434 TRP 0.022 0.002 TRP Y 36 HIS 0.007 0.001 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00447 (13194) covalent geometry : angle 0.55350 (17967) SS BOND : bond 0.00374 ( 8) SS BOND : angle 1.79748 ( 16) hydrogen bonds : bond 0.04392 ( 539) hydrogen bonds : angle 4.62752 ( 1482) link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 2.02699 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11390.86 seconds wall clock time: 192 minutes 56.59 seconds (11576.59 seconds total)