Starting phenix.real_space_refine on Sun Jun 22 15:56:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xw6_33492/06_2025/7xw6_33492_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xw6_33492/06_2025/7xw6_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_33492/06_2025/7xw6_33492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xw6_33492/06_2025/7xw6_33492.map" model { file = "/net/cci-nas-00/data/ceres_data/7xw6_33492/06_2025/7xw6_33492_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xw6_33492/06_2025/7xw6_33492_neut_trim.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.23, per 1000 atoms: 0.53 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: 6.97 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.77 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: 10.54 Time building geometry restraints manager: 8.45 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: 1.850 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: 0.450 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 58.840 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.880 ------------------------------------------------------------------------------- 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 : 0.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (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 TRP 0.119 0.022 TRP R 488 HIS 0.013 0.004 HIS R 282 PHE 0.064 0.014 PHE A 222 TYR 0.111 0.018 TYR Y 56 ARG 0.011 0.001 ARG B 48 Details of bonding type rmsd link_NAG-ASN : bond 0.01426 ( 4) link_NAG-ASN : angle 4.75340 ( 12) hydrogen bonds : bond 0.17048 ( 539) hydrogen bonds : angle 7.18359 ( 1482) SS BOND : bond 0.01315 ( 8) SS BOND : angle 2.60241 ( 16) covalent geometry : bond 0.01326 (13194) covalent geometry : angle 1.79004 (17967) *********************** 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 : 1.867 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: A 60 MET cc_start: 0.7339 (mmm) cc_final: 0.7052 (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 134 PHE cc_start: 0.8013 (m-80) cc_final: 0.7798 (m-80) 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: 0.7916 (t80) REVERT: R 658 ASN cc_start: 0.8600 (m-40) cc_final: 0.8353 (m-40) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 2.2536 time to fit residues: 941.9539 Evaluate side-chains 325 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.156946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126885 restraints weight = 50239.260| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.26 r_work: 0.3551 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 13206 Z= 0.176 Angle : 0.669 7.879 17995 Z= 0.354 Chirality : 0.044 0.382 2072 Planarity : 0.005 0.052 2169 Dihedral : 7.268 76.622 2974 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.85 % Allowed : 9.27 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1530 helix: 1.26 (0.26), residues: 392 sheet: 0.09 (0.26), residues: 368 loop : -0.30 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.008 0.002 HIS R 105 PHE 0.022 0.002 PHE N 29 TYR 0.017 0.002 TYR R 667 ARG 0.005 0.001 ARG R 625 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 4) link_NAG-ASN : angle 3.66881 ( 12) hydrogen bonds : bond 0.05421 ( 539) hydrogen bonds : angle 5.56042 ( 1482) SS BOND : bond 0.00735 ( 8) SS BOND : angle 2.68472 ( 16) covalent geometry : bond 0.00400 (13194) covalent geometry : angle 0.65747 (17967) *********************** 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 365 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 340 time to evaluate : 2.082 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: A 59 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7757 (mp10) REVERT: A 60 MET cc_start: 0.7676 (mmm) cc_final: 0.7430 (mtp) REVERT: A 371 ASP cc_start: 0.8345 (t70) cc_final: 0.8011 (t0) REVERT: B 99 TRP cc_start: 0.8164 (m-90) cc_final: 0.7436 (m-90) REVERT: G 17 GLU cc_start: 0.8097 (tp30) cc_final: 0.7867 (tp30) REVERT: G 24 ASN cc_start: 0.7688 (m-40) cc_final: 0.7198 (m-40) REVERT: L 35 TRP cc_start: 0.7886 (m100) cc_final: 0.7114 (m100) REVERT: N 21 SER cc_start: 0.8240 (t) cc_final: 0.7967 (p) REVERT: N 31 ASN cc_start: 0.8316 (m110) cc_final: 0.8006 (m110) REVERT: N 113 THR cc_start: 0.8840 (t) cc_final: 0.8614 (p) REVERT: R 30 GLU cc_start: 0.6062 (tm-30) cc_final: 0.5812 (tm-30) REVERT: R 123 LYS cc_start: 0.8357 (pttt) cc_final: 0.7923 (pttt) REVERT: R 134 PHE cc_start: 0.8344 (m-80) cc_final: 0.8126 (m-80) REVERT: R 239 THR cc_start: 0.8664 (p) cc_final: 0.8454 (m) REVERT: R 460 ASP cc_start: 0.8025 (m-30) cc_final: 0.7757 (m-30) REVERT: R 463 MET cc_start: 0.8530 (tpp) cc_final: 0.8311 (tpp) REVERT: R 465 MET cc_start: 0.8274 (tpt) cc_final: 0.7931 (tpt) REVERT: R 642 PHE cc_start: 0.8221 (t80) cc_final: 0.8019 (t80) REVERT: Y 59 TYR cc_start: 0.8239 (m-80) cc_final: 0.8001 (m-80) REVERT: Y 91 TYR cc_start: 0.7246 (m-80) cc_final: 0.6958 (m-80) outliers start: 25 outliers final: 11 residues processed: 347 average time/residue: 2.3569 time to fit residues: 904.7252 Evaluate side-chains 328 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 317 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 106 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 257 GLN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 120 GLN ** R 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 ASN R 186 ASN Y 66 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.124295 restraints weight = 50016.522| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.24 r_work: 0.3513 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13206 Z= 0.237 Angle : 0.635 6.790 17995 Z= 0.338 Chirality : 0.044 0.362 2072 Planarity : 0.004 0.055 2169 Dihedral : 6.655 60.530 2974 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.78 % Allowed : 12.82 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1530 helix: 1.57 (0.26), residues: 392 sheet: -0.12 (0.25), residues: 389 loop : -0.36 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 47 HIS 0.010 0.002 HIS R 105 PHE 0.020 0.002 PHE B 235 TYR 0.018 0.002 TYR L 49 ARG 0.009 0.001 ARG A 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 4) link_NAG-ASN : angle 3.13029 ( 12) hydrogen bonds : bond 0.05181 ( 539) hydrogen bonds : angle 5.21799 ( 1482) SS BOND : bond 0.00433 ( 8) SS BOND : angle 2.13963 ( 16) covalent geometry : bond 0.00545 (13194) covalent geometry : angle 0.62701 (17967) *********************** 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 353 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 329 time to evaluate : 1.889 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: A 59 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7791 (mp10) REVERT: A 256 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6737 (tp) REVERT: A 371 ASP cc_start: 0.8421 (t70) cc_final: 0.8110 (t0) REVERT: B 99 TRP cc_start: 0.8255 (m-90) cc_final: 0.7950 (m100) REVERT: G 17 GLU cc_start: 0.8015 (tp30) cc_final: 0.7743 (tp30) REVERT: G 24 ASN cc_start: 0.7662 (m-40) cc_final: 0.7191 (m-40) REVERT: L 35 TRP cc_start: 0.8000 (m100) cc_final: 0.7379 (m100) REVERT: N 21 SER cc_start: 0.8342 (t) cc_final: 0.7945 (p) REVERT: N 31 ASN cc_start: 0.8352 (m110) cc_final: 0.8051 (m110) REVERT: R 30 GLU cc_start: 0.6009 (tm-30) cc_final: 0.5669 (tm-30) REVERT: R 123 LYS cc_start: 0.8428 (pttt) cc_final: 0.7989 (pttt) REVERT: R 239 THR cc_start: 0.8711 (p) cc_final: 0.8500 (m) REVERT: R 465 MET cc_start: 0.8366 (tpt) cc_final: 0.8010 (tpt) REVERT: R 657 SER cc_start: 0.8572 (m) cc_final: 0.8289 (t) REVERT: Y 91 TYR cc_start: 0.7258 (m-80) cc_final: 0.6938 (m-80) outliers start: 24 outliers final: 14 residues processed: 334 average time/residue: 2.4297 time to fit residues: 892.7091 Evaluate side-chains 333 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 318 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain L residue 58 VAL 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 104 THR 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 68 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 155 ASN B 237 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.155330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125297 restraints weight = 50593.662| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.27 r_work: 0.3532 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13206 Z= 0.137 Angle : 0.552 5.744 17995 Z= 0.290 Chirality : 0.041 0.352 2072 Planarity : 0.004 0.057 2169 Dihedral : 6.318 60.500 2974 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.48 % Allowed : 14.31 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1530 helix: 1.96 (0.27), residues: 386 sheet: -0.22 (0.25), residues: 391 loop : -0.30 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 47 HIS 0.008 0.001 HIS R 105 PHE 0.013 0.001 PHE A 222 TYR 0.012 0.001 TYR R 582 ARG 0.006 0.000 ARG L 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 4) link_NAG-ASN : angle 2.81597 ( 12) hydrogen bonds : bond 0.04431 ( 539) hydrogen bonds : angle 4.96629 ( 1482) SS BOND : bond 0.00684 ( 8) SS BOND : angle 1.51049 ( 16) covalent geometry : bond 0.00310 (13194) covalent geometry : angle 0.54554 (17967) *********************** 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 353 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 333 time to evaluate : 2.067 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: 0.8135 (mm-40) cc_final: 0.7784 (mp10) REVERT: A 256 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6579 (tt) REVERT: A 324 VAL cc_start: 0.7982 (p) cc_final: 0.7583 (m) REVERT: A 371 ASP cc_start: 0.8378 (t70) cc_final: 0.8067 (t0) REVERT: B 99 TRP cc_start: 0.8254 (m-90) cc_final: 0.7750 (m100) REVERT: G 17 GLU cc_start: 0.8019 (tp30) cc_final: 0.7740 (tp30) REVERT: G 24 ASN cc_start: 0.7677 (m-40) cc_final: 0.7231 (m-40) REVERT: L 35 TRP cc_start: 0.7915 (m100) cc_final: 0.7242 (m100) REVERT: N 21 SER cc_start: 0.8239 (t) cc_final: 0.7850 (p) REVERT: N 31 ASN cc_start: 0.8320 (m110) cc_final: 0.7995 (m110) REVERT: R 30 GLU cc_start: 0.6095 (tm-30) cc_final: 0.5779 (tm-30) REVERT: R 83 VAL cc_start: 0.7838 (t) cc_final: 0.7615 (t) REVERT: R 123 LYS cc_start: 0.8437 (pttt) cc_final: 0.8002 (pttt) REVERT: R 239 THR cc_start: 0.8685 (p) cc_final: 0.8443 (m) REVERT: R 420 VAL cc_start: 0.8647 (p) cc_final: 0.8352 (t) REVERT: R 463 MET cc_start: 0.8420 (tpp) cc_final: 0.8038 (tpp) REVERT: R 465 MET cc_start: 0.8319 (tpt) cc_final: 0.7963 (tpt) REVERT: R 657 SER cc_start: 0.8569 (m) cc_final: 0.8347 (t) REVERT: Y 36 TRP cc_start: 0.7324 (m100) cc_final: 0.7030 (m100) REVERT: Y 66 HIS cc_start: 0.7021 (m170) cc_final: 0.6698 (m170) REVERT: Y 89 MET cc_start: 0.4954 (tpp) cc_final: 0.4732 (tpt) REVERT: Y 91 TYR cc_start: 0.7264 (m-80) cc_final: 0.6971 (m-80) outliers start: 20 outliers final: 10 residues processed: 342 average time/residue: 2.3200 time to fit residues: 877.3140 Evaluate side-chains 326 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 315 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 122 SER Chi-restraints excluded: chain B residue 218 CYS 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 166 SER 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 87 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 36 ASN B 75 GLN N 3 GLN R 187 ASN R 484 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122582 restraints weight = 50109.458| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.23 r_work: 0.3486 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13206 Z= 0.279 Angle : 0.623 7.778 17995 Z= 0.329 Chirality : 0.044 0.365 2072 Planarity : 0.004 0.048 2169 Dihedral : 6.457 55.992 2974 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.30 % Allowed : 14.97 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1530 helix: 1.66 (0.26), residues: 389 sheet: -0.26 (0.25), residues: 392 loop : -0.47 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 47 HIS 0.010 0.002 HIS R 105 PHE 0.020 0.002 PHE N 108 TYR 0.019 0.002 TYR R 582 ARG 0.006 0.001 ARG R 625 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 4) link_NAG-ASN : angle 2.77211 ( 12) hydrogen bonds : bond 0.05094 ( 539) hydrogen bonds : angle 5.01616 ( 1482) SS BOND : bond 0.00458 ( 8) SS BOND : angle 2.42874 ( 16) covalent geometry : bond 0.00641 (13194) covalent geometry : angle 0.61499 (17967) *********************** 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 357 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 326 time to evaluate : 2.587 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: A 59 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7897 (mp10) REVERT: A 324 VAL cc_start: 0.8085 (p) cc_final: 0.7706 (m) REVERT: A 371 ASP cc_start: 0.8412 (t70) cc_final: 0.8116 (t0) REVERT: B 99 TRP cc_start: 0.8288 (m-90) cc_final: 0.7937 (m100) REVERT: B 217 MET cc_start: 0.7469 (mmm) cc_final: 0.7169 (mmm) REVERT: G 17 GLU cc_start: 0.7981 (tp30) cc_final: 0.7679 (tp30) REVERT: G 24 ASN cc_start: 0.7682 (m-40) cc_final: 0.7253 (m-40) REVERT: L 35 TRP cc_start: 0.8032 (m100) cc_final: 0.7458 (m100) REVERT: N 21 SER cc_start: 0.8302 (t) cc_final: 0.7873 (p) REVERT: N 31 ASN cc_start: 0.8375 (m110) cc_final: 0.8077 (m110) REVERT: R 30 GLU cc_start: 0.6173 (tm-30) cc_final: 0.5808 (tm-30) REVERT: R 83 VAL cc_start: 0.8138 (t) cc_final: 0.7900 (t) REVERT: R 463 MET cc_start: 0.8425 (tpp) cc_final: 0.8157 (tpp) REVERT: R 465 MET cc_start: 0.8335 (tpt) cc_final: 0.7977 (tpt) REVERT: R 528 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7820 (mmm160) REVERT: R 626 MET cc_start: 0.7954 (mtp) cc_final: 0.7753 (mtt) REVERT: R 657 SER cc_start: 0.8575 (m) cc_final: 0.8363 (t) REVERT: Y 66 HIS cc_start: 0.7300 (m170) cc_final: 0.7044 (m170) outliers start: 31 outliers final: 15 residues processed: 342 average time/residue: 2.3501 time to fit residues: 897.8274 Evaluate side-chains 326 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 311 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 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 209 LYS Chi-restraints excluded: chain R residue 470 ILE 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 147 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.154488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124613 restraints weight = 50105.565| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.25 r_work: 0.3521 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13206 Z= 0.132 Angle : 0.540 5.660 17995 Z= 0.283 Chirality : 0.041 0.355 2072 Planarity : 0.004 0.052 2169 Dihedral : 6.181 56.145 2974 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 1.70 % Allowed : 16.60 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1530 helix: 2.00 (0.27), residues: 387 sheet: -0.35 (0.25), residues: 394 loop : -0.39 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Y 36 HIS 0.006 0.001 HIS R 105 PHE 0.019 0.001 PHE A 222 TYR 0.015 0.001 TYR R 482 ARG 0.007 0.000 ARG L 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 4) link_NAG-ASN : angle 2.53472 ( 12) hydrogen bonds : bond 0.04225 ( 539) hydrogen bonds : angle 4.80844 ( 1482) SS BOND : bond 0.00255 ( 8) SS BOND : angle 1.66734 ( 16) covalent geometry : bond 0.00300 (13194) covalent geometry : angle 0.53363 (17967) *********************** 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 347 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 324 time to evaluate : 1.911 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: A 59 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7870 (mp10) REVERT: A 371 ASP cc_start: 0.8427 (t70) cc_final: 0.8109 (t0) REVERT: B 51 LEU cc_start: 0.8164 (mp) cc_final: 0.7954 (mt) REVERT: B 99 TRP cc_start: 0.8282 (m-90) cc_final: 0.7855 (m100) REVERT: B 217 MET cc_start: 0.7264 (mmm) cc_final: 0.6986 (mmm) REVERT: G 17 GLU cc_start: 0.7987 (tp30) cc_final: 0.7682 (tp30) REVERT: G 24 ASN cc_start: 0.7712 (m-40) cc_final: 0.7300 (m-40) REVERT: L 35 TRP cc_start: 0.7922 (m100) cc_final: 0.7350 (m100) REVERT: N 21 SER cc_start: 0.8253 (t) cc_final: 0.7848 (p) REVERT: N 31 ASN cc_start: 0.8309 (m110) cc_final: 0.8011 (m110) REVERT: R 30 GLU cc_start: 0.6105 (tm-30) cc_final: 0.5777 (tm-30) REVERT: R 83 VAL cc_start: 0.7851 (t) cc_final: 0.7630 (t) REVERT: R 123 LYS cc_start: 0.8429 (pttt) cc_final: 0.8047 (pttt) REVERT: R 129 LYS cc_start: 0.8174 (pttp) cc_final: 0.7858 (ptpp) REVERT: R 180 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8242 (tt) REVERT: R 182 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8223 (mt) REVERT: R 420 VAL cc_start: 0.8649 (p) cc_final: 0.8369 (t) REVERT: R 463 MET cc_start: 0.8444 (tpp) cc_final: 0.7993 (tpp) REVERT: R 465 MET cc_start: 0.8318 (tpt) cc_final: 0.7971 (tpt) REVERT: R 528 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7825 (mmm160) REVERT: R 657 SER cc_start: 0.8586 (m) cc_final: 0.8373 (t) REVERT: Y 66 HIS cc_start: 0.7284 (m170) cc_final: 0.7011 (m170) REVERT: Y 91 TYR cc_start: 0.7259 (m-80) cc_final: 0.6969 (m-80) outliers start: 23 outliers final: 13 residues processed: 341 average time/residue: 2.3166 time to fit residues: 873.0273 Evaluate side-chains 327 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 312 time to evaluate : 2.172 ------------------------------------------------------------------------------- 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 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 180 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.153352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123455 restraints weight = 50171.390| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.24 r_work: 0.3503 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13206 Z= 0.191 Angle : 0.559 6.069 17995 Z= 0.293 Chirality : 0.041 0.359 2072 Planarity : 0.004 0.052 2169 Dihedral : 6.165 56.084 2974 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 1.85 % Allowed : 17.05 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1530 helix: 1.83 (0.27), residues: 394 sheet: -0.33 (0.25), residues: 394 loop : -0.47 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 47 HIS 0.008 0.001 HIS R 105 PHE 0.020 0.001 PHE A 222 TYR 0.016 0.001 TYR R 482 ARG 0.007 0.000 ARG L 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 4) link_NAG-ASN : angle 2.40834 ( 12) hydrogen bonds : bond 0.04472 ( 539) hydrogen bonds : angle 4.79060 ( 1482) SS BOND : bond 0.00418 ( 8) SS BOND : angle 1.98791 ( 16) covalent geometry : bond 0.00439 (13194) covalent geometry : angle 0.55256 (17967) *********************** 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 338 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 1.994 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: A 59 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7850 (mp10) REVERT: B 51 LEU cc_start: 0.8187 (mp) cc_final: 0.7980 (mt) REVERT: B 217 MET cc_start: 0.7383 (mmm) cc_final: 0.7121 (mmm) REVERT: G 17 GLU cc_start: 0.7967 (tp30) cc_final: 0.7664 (tp30) REVERT: G 24 ASN cc_start: 0.7705 (m-40) cc_final: 0.7304 (m-40) REVERT: L 35 TRP cc_start: 0.7996 (m100) cc_final: 0.7458 (m100) REVERT: N 21 SER cc_start: 0.8283 (t) cc_final: 0.7808 (p) REVERT: N 31 ASN cc_start: 0.8326 (m110) cc_final: 0.8022 (m110) REVERT: N 80 TYR cc_start: 0.7746 (m-80) cc_final: 0.6927 (m-80) REVERT: R 30 GLU cc_start: 0.6191 (tm-30) cc_final: 0.5898 (tm-30) REVERT: R 83 VAL cc_start: 0.8012 (t) cc_final: 0.7786 (t) REVERT: R 182 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8228 (mt) REVERT: R 463 MET cc_start: 0.8450 (tpp) cc_final: 0.7944 (tpp) REVERT: R 465 MET cc_start: 0.8330 (tpt) cc_final: 0.7992 (tpt) REVERT: R 480 GLU cc_start: 0.7942 (pt0) cc_final: 0.7578 (pp20) REVERT: R 657 SER cc_start: 0.8618 (m) cc_final: 0.8368 (t) REVERT: Y 91 TYR cc_start: 0.7267 (m-80) cc_final: 0.6978 (m-80) outliers start: 25 outliers final: 18 residues processed: 330 average time/residue: 2.7069 time to fit residues: 997.5252 Evaluate side-chains 331 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 312 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 223 THR 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 111 THR 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 180 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE 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 91 optimal weight: 4.9990 chunk 115 optimal weight: 0.0060 chunk 71 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.153079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123638 restraints weight = 49822.025| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.21 r_work: 0.3505 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13206 Z= 0.191 Angle : 0.559 5.867 17995 Z= 0.293 Chirality : 0.041 0.360 2072 Planarity : 0.004 0.055 2169 Dihedral : 6.113 56.504 2974 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 1.78 % Allowed : 17.64 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1530 helix: 1.72 (0.27), residues: 401 sheet: -0.34 (0.25), residues: 394 loop : -0.52 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 47 HIS 0.007 0.001 HIS R 105 PHE 0.020 0.002 PHE A 222 TYR 0.018 0.001 TYR R 482 ARG 0.007 0.000 ARG L 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 4) link_NAG-ASN : angle 2.32376 ( 12) hydrogen bonds : bond 0.04444 ( 539) hydrogen bonds : angle 4.77421 ( 1482) SS BOND : bond 0.00364 ( 8) SS BOND : angle 1.76793 ( 16) covalent geometry : bond 0.00440 (13194) covalent geometry : angle 0.55372 (17967) *********************** 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 345 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 321 time to evaluate : 2.025 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: A 59 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7865 (mp10) REVERT: B 51 LEU cc_start: 0.8189 (mp) cc_final: 0.7984 (mt) REVERT: B 217 MET cc_start: 0.7419 (mmm) cc_final: 0.7139 (mmm) REVERT: G 17 GLU cc_start: 0.7953 (tp30) cc_final: 0.7642 (tp30) REVERT: G 24 ASN cc_start: 0.7719 (m-40) cc_final: 0.7348 (m-40) REVERT: L 35 TRP cc_start: 0.7994 (m100) cc_final: 0.7450 (m100) REVERT: N 21 SER cc_start: 0.8256 (t) cc_final: 0.7795 (p) REVERT: N 31 ASN cc_start: 0.8327 (m110) cc_final: 0.8037 (m110) REVERT: N 80 TYR cc_start: 0.7742 (m-80) cc_final: 0.6931 (m-80) REVERT: R 30 GLU cc_start: 0.6179 (tm-30) cc_final: 0.5888 (tm-30) REVERT: R 83 VAL cc_start: 0.7971 (t) cc_final: 0.7747 (t) REVERT: R 123 LYS cc_start: 0.8451 (pttt) cc_final: 0.8054 (pttt) REVERT: R 182 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8225 (mt) REVERT: R 262 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8327 (mtmm) REVERT: R 420 VAL cc_start: 0.8654 (p) cc_final: 0.8392 (t) REVERT: R 463 MET cc_start: 0.8433 (tpp) cc_final: 0.8136 (tpp) REVERT: R 465 MET cc_start: 0.8312 (tpt) cc_final: 0.7969 (tpt) REVERT: R 657 SER cc_start: 0.8621 (m) cc_final: 0.8361 (t) REVERT: Y 91 TYR cc_start: 0.7277 (m-80) cc_final: 0.6986 (m-80) outliers start: 24 outliers final: 16 residues processed: 337 average time/residue: 2.2631 time to fit residues: 842.7743 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 : 1.840 ------------------------------------------------------------------------------- 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 L residue 65 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 111 THR 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 180 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE 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 3 optimal weight: 0.6980 chunk 65 optimal weight: 0.0030 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.153872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124407 restraints weight = 50138.602| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.24 r_work: 0.3508 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13206 Z= 0.142 Angle : 0.537 6.193 17995 Z= 0.280 Chirality : 0.040 0.356 2072 Planarity : 0.004 0.057 2169 Dihedral : 5.969 58.238 2974 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.63 % Allowed : 17.72 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1530 helix: 1.93 (0.27), residues: 398 sheet: -0.32 (0.25), residues: 399 loop : -0.44 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 47 HIS 0.006 0.001 HIS R 105 PHE 0.020 0.001 PHE A 222 TYR 0.021 0.001 TYR R 482 ARG 0.008 0.000 ARG L 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 2.18469 ( 12) hydrogen bonds : bond 0.04160 ( 539) hydrogen bonds : angle 4.68537 ( 1482) SS BOND : bond 0.00327 ( 8) SS BOND : angle 1.50403 ( 16) covalent geometry : bond 0.00327 (13194) covalent geometry : angle 0.53297 (17967) *********************** 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 341 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 319 time to evaluate : 1.854 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: A 59 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7862 (mp10) REVERT: B 217 MET cc_start: 0.7367 (mmm) cc_final: 0.7091 (mmm) REVERT: G 17 GLU cc_start: 0.7956 (tp30) cc_final: 0.7642 (tp30) REVERT: G 58 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7496 (mm-30) REVERT: L 35 TRP cc_start: 0.7924 (m100) cc_final: 0.7381 (m100) REVERT: N 21 SER cc_start: 0.8242 (t) cc_final: 0.7787 (p) REVERT: N 31 ASN cc_start: 0.8307 (m110) cc_final: 0.8023 (m110) REVERT: N 80 TYR cc_start: 0.7682 (m-80) cc_final: 0.6878 (m-80) REVERT: R 83 VAL cc_start: 0.7940 (t) cc_final: 0.7719 (t) REVERT: R 123 LYS cc_start: 0.8427 (pttt) cc_final: 0.8026 (pttt) REVERT: R 134 PHE cc_start: 0.8662 (m-80) cc_final: 0.8426 (m-80) REVERT: R 182 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8201 (mt) REVERT: R 262 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8316 (mtmm) REVERT: R 463 MET cc_start: 0.8425 (tpp) cc_final: 0.8141 (tpp) REVERT: R 465 MET cc_start: 0.8331 (tpt) cc_final: 0.7987 (tpt) REVERT: R 657 SER cc_start: 0.8614 (m) cc_final: 0.8351 (t) REVERT: Y 91 TYR cc_start: 0.7269 (m-80) cc_final: 0.6993 (m-80) outliers start: 22 outliers final: 18 residues processed: 334 average time/residue: 2.2228 time to fit residues: 824.4616 Evaluate side-chains 333 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 314 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 223 THR 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 N residue 96 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 66 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124979 restraints weight = 50202.733| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.20 r_work: 0.3524 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13206 Z= 0.131 Angle : 0.534 6.440 17995 Z= 0.277 Chirality : 0.040 0.357 2072 Planarity : 0.004 0.071 2169 Dihedral : 5.851 59.769 2974 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.41 % Allowed : 18.16 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1530 helix: 1.98 (0.27), residues: 397 sheet: -0.27 (0.25), residues: 393 loop : -0.45 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Y 36 HIS 0.005 0.001 HIS R 105 PHE 0.019 0.001 PHE A 222 TYR 0.022 0.001 TYR R 482 ARG 0.011 0.000 ARG R 625 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 4) link_NAG-ASN : angle 2.05129 ( 12) hydrogen bonds : bond 0.04068 ( 539) hydrogen bonds : angle 4.61816 ( 1482) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.40119 ( 16) covalent geometry : bond 0.00300 (13194) covalent geometry : angle 0.52976 (17967) ********************** 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 334 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 315 time to evaluate : 2.096 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: A 59 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7830 (mp10) REVERT: B 217 MET cc_start: 0.7414 (mmm) cc_final: 0.7137 (mmm) REVERT: G 17 GLU cc_start: 0.7958 (tp30) cc_final: 0.7646 (tp30) REVERT: G 58 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7419 (mm-30) REVERT: L 35 TRP cc_start: 0.7906 (m100) cc_final: 0.7377 (m100) REVERT: N 21 SER cc_start: 0.8245 (t) cc_final: 0.7801 (p) REVERT: N 31 ASN cc_start: 0.8297 (m110) cc_final: 0.8010 (m110) REVERT: N 80 TYR cc_start: 0.7640 (m-80) cc_final: 0.6855 (m-80) REVERT: R 83 VAL cc_start: 0.7878 (t) cc_final: 0.7664 (t) REVERT: R 123 LYS cc_start: 0.8412 (pttt) cc_final: 0.8046 (pttt) REVERT: R 134 PHE cc_start: 0.8642 (m-80) cc_final: 0.8425 (m-80) REVERT: R 182 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8187 (mt) REVERT: R 207 LEU cc_start: 0.7834 (pp) cc_final: 0.7566 (pt) REVERT: R 262 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8309 (mtmm) REVERT: R 463 MET cc_start: 0.8418 (tpp) cc_final: 0.8143 (tpp) REVERT: R 465 MET cc_start: 0.8332 (tpt) cc_final: 0.7993 (tpt) REVERT: R 657 SER cc_start: 0.8607 (m) cc_final: 0.8347 (t) REVERT: Y 91 TYR cc_start: 0.7264 (m-80) cc_final: 0.6988 (m-80) outliers start: 19 outliers final: 16 residues processed: 327 average time/residue: 2.6689 time to fit residues: 974.8809 Evaluate side-chains 331 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 314 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 137 ARG 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 N residue 96 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 209 LYS Chi-restraints excluded: chain R residue 470 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 46 optimal weight: 0.1980 chunk 121 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.154558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.125430 restraints weight = 50176.005| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.21 r_work: 0.3523 rms_B_bonded: 2.55 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: 0.7741 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13206 Z= 0.122 Angle : 0.515 6.183 17995 Z= 0.269 Chirality : 0.040 0.357 2072 Planarity : 0.004 0.078 2169 Dihedral : 5.650 55.199 2974 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.26 % Allowed : 18.16 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1530 helix: 2.03 (0.27), residues: 399 sheet: -0.22 (0.25), residues: 393 loop : -0.37 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Y 36 HIS 0.005 0.001 HIS R 105 PHE 0.029 0.001 PHE R 434 TYR 0.024 0.001 TYR R 482 ARG 0.011 0.000 ARG L 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 4) link_NAG-ASN : angle 1.87709 ( 12) hydrogen bonds : bond 0.03912 ( 539) hydrogen bonds : angle 4.53430 ( 1482) SS BOND : bond 0.00239 ( 8) SS BOND : angle 1.25709 ( 16) covalent geometry : bond 0.00280 (13194) covalent geometry : angle 0.51138 (17967) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23410.38 seconds wall clock time: 401 minutes 58.00 seconds (24118.00 seconds total)