Starting phenix.real_space_refine on Thu Aug 6 07:00:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpa_34929/08_2026/8hpa_34929.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpa_34929/08_2026/8hpa_34929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hpa_34929/08_2026/8hpa_34929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpa_34929/08_2026/8hpa_34929.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hpa_34929/08_2026/8hpa_34929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpa_34929/08_2026/8hpa_34929.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 P 32 5.49 5 S 72 5.16 5 C 8943 2.51 5 N 2353 2.21 5 O 2722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14122 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 8208 Classifications: {'peptide': 1004} Link IDs: {'CIS': 1, 'PTRANS': 37, 'TRANS': 965} Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3467 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "E" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 382 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 293 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Residues with excluded nonbonded symmetry interactions: 31 residue: pdb=" N GLU A 856 " occ=0.41 ... (7 atoms not shown) pdb=" OE2 GLU A 856 " occ=0.41 residue: pdb=" N GLY A 857 " occ=0.41 ... (2 atoms not shown) pdb=" O GLY A 857 " occ=0.41 residue: pdb=" N ARG A 858 " occ=0.32 ... (9 atoms not shown) pdb=" NH2 ARG A 858 " occ=0.32 residue: pdb=" N MET A 859 " occ=0.42 ... (6 atoms not shown) pdb=" CE MET A 859 " occ=0.42 residue: pdb=" N ASN A 860 " occ=0.35 ... (6 atoms not shown) pdb=" ND2 ASN A 860 " occ=0.35 residue: pdb=" N SER A 861 " occ=0.16 ... (4 atoms not shown) pdb=" OG SER A 861 " occ=0.16 residue: pdb=" N ASN A 862 " occ=0.26 ... (6 atoms not shown) pdb=" ND2 ASN A 862 " occ=0.26 residue: pdb=" N GLN A 863 " occ=0.45 ... (7 atoms not shown) pdb=" NE2 GLN A 863 " occ=0.45 residue: pdb=" N GLY C 46 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY C 46 " occ=0.88 residue: pdb=" N VAL C 47 " occ=0.62 ... (5 atoms not shown) pdb=" CG2 VAL C 47 " occ=0.62 residue: pdb=" N GLN C 48 " occ=0.77 ... (7 atoms not shown) pdb=" NE2 GLN C 48 " occ=0.77 residue: pdb=" N LYS C 49 " occ=0.55 ... (7 atoms not shown) pdb=" NZ LYS C 49 " occ=0.55 ... (remaining 19 not shown) Time building chain proxies: 2.19, per 1000 atoms: 0.16 Number of scatterers: 14122 At special positions: 0 Unit cell: (113.4, 122.64, 143.64, 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 72 16.00 P 32 15.00 O 2722 8.00 N 2353 7.00 C 8943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 370.1 milliseconds 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3154 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 37.8% alpha, 14.0% beta 1 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.645A pdb=" N CYS A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 149' Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 350 through 354 removed outlier: 4.240A pdb=" N PHE A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.641A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.503A pdb=" N LYS A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.632A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.743A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 644 removed outlier: 3.598A pdb=" N ARG A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 666 removed outlier: 3.665A pdb=" N TYR A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.821A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 764 through 782 Processing helix chain 'A' and resid 828 through 832 Processing helix chain 'A' and resid 837 through 856 removed outlier: 3.676A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 879 Processing helix chain 'A' and resid 905 through 918 removed outlier: 3.703A pdb=" N TYR A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 973 removed outlier: 3.535A pdb=" N PHE A 972 " --> pdb=" O TYR A 968 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 968 through 973' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 985 through 997 removed outlier: 4.149A pdb=" N CYS A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 20 removed outlier: 6.126A pdb=" N GLU C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 24 through 39 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 108 through 115 Processing helix chain 'C' and resid 149 through 159 removed outlier: 5.363A pdb=" N ALA C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.651A pdb=" N ASP C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 317 through 324 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 406 Processing helix chain 'C' and resid 406 through 426 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.667A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.990A pdb=" N ILE B 112 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.284A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.554A pdb=" N VAL B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.587A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 7 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A 136 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.792A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.018A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.052A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU A 168 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A 186 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP A 166 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR A 188 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE A 164 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR A 190 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A 162 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 372 removed outlier: 3.577A pdb=" N GLY A 372 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 415 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE A 410 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 404 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS A 403 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 395 " --> pdb=" O CYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 706 removed outlier: 7.048A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY A 750 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N MET A 800 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS A 805 " --> pdb=" O MET A 800 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 removed outlier: 3.515A pdb=" N ARG A 894 " --> pdb=" O TYR A 928 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 82 Processing sheet with id=AB3, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.533A pdb=" N ILE C 238 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 375 through 377 Processing sheet with id=AB5, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AB6, first strand: chain 'B' and resid 115 through 120 removed outlier: 6.732A pdb=" N GLY B 115 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG B 61 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR B 156 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY B 179 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS B 157 " --> pdb=" O GLY B 179 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4173 1.34 - 1.45: 2377 1.45 - 1.57: 7773 1.57 - 1.69: 63 1.69 - 1.81: 110 Bond restraints: 14496 Sorted by residual: bond pdb=" C3' DT D -6 " pdb=" C2' DT D -6 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C1' DC D -13 " pdb=" N1 DC D -13 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.82e+00 bond pdb=" C1' DC D -8 " pdb=" N1 DC D -8 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.21e+00 bond pdb=" C3' DA E -2 " pdb=" C2' DA E -2 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.92e+00 bond pdb=" C1' DC D 1 " pdb=" N1 DC D 1 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.46e+00 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 19400 1.95 - 3.91: 287 3.91 - 5.86: 38 5.86 - 7.81: 3 7.81 - 9.77: 3 Bond angle restraints: 19731 Sorted by residual: angle pdb=" C SER A 884 " pdb=" CA SER A 884 " pdb=" CB SER A 884 " ideal model delta sigma weight residual 117.23 111.15 6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N3 DT E 3 " pdb=" C4 DT E 3 " pdb=" O4 DT E 3 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT D -7 " pdb=" C4 DT D -7 " pdb=" O4 DT D -7 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT E -11 " pdb=" C4 DT E -11 " pdb=" O4 DT E -11 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT D -10 " pdb=" C4 DT D -10 " pdb=" O4 DT D -10 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 19726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 8434 35.91 - 71.81: 220 71.81 - 107.72: 11 107.72 - 143.63: 1 143.63 - 179.53: 3 Dihedral angle restraints: 8669 sinusoidal: 3777 harmonic: 4892 Sorted by residual: dihedral pdb=" CA GLY A 325 " pdb=" C GLY A 325 " pdb=" N THR A 326 " pdb=" CA THR A 326 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DA D -11 " pdb=" C3' DA D -11 " pdb=" O3' DA D -11 " pdb=" P DT D -10 " ideal model delta sinusoidal sigma weight residual -140.00 39.53 -179.53 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA E -2 " pdb=" C3' DA E -2 " pdb=" O3' DA E -2 " pdb=" P DA E -1 " ideal model delta sinusoidal sigma weight residual -140.00 30.28 -170.28 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1291 0.030 - 0.059: 591 0.059 - 0.089: 182 0.089 - 0.119: 92 0.119 - 0.148: 27 Chirality restraints: 2183 Sorted by residual: chirality pdb=" CB ILE C 45 " pdb=" CA ILE C 45 " pdb=" CG1 ILE C 45 " pdb=" CG2 ILE C 45 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CB ILE C 245 " pdb=" CA ILE C 245 " pdb=" CG1 ILE C 245 " pdb=" CG2 ILE C 245 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" P DA E -1 " pdb=" OP1 DA E -1 " pdb=" OP2 DA E -1 " pdb=" O5' DA E -1 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 2180 not shown) Planarity restraints: 2397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 9 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 10 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 918 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 919 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 919 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 919 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 149 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C VAL C 149 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL C 149 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN C 150 " 0.010 2.00e-02 2.50e+03 ... (remaining 2394 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 363 2.70 - 3.25: 13749 3.25 - 3.80: 21780 3.80 - 4.35: 28715 4.35 - 4.90: 47162 Nonbonded interactions: 111769 Sorted by model distance: nonbonded pdb=" OH TYR A 40 " pdb=" O LYS A 96 " model vdw 2.144 3.040 nonbonded pdb=" O GLU A 339 " pdb=" OH TYR A 344 " model vdw 2.210 3.040 nonbonded pdb=" O ASP C 72 " pdb=" OH TYR C 76 " model vdw 2.211 3.040 nonbonded pdb=" O LYS A 796 " pdb=" OG1 THR A 808 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 81 " pdb=" OD1 ASN B 83 " model vdw 2.253 3.040 ... (remaining 111764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 4.820 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.850 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14496 Z= 0.183 Angle : 0.566 9.769 19731 Z= 0.344 Chirality : 0.042 0.148 2183 Planarity : 0.004 0.056 2397 Dihedral : 15.988 179.534 5515 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.26 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.21), residues: 1642 helix: 1.12 (0.23), residues: 563 sheet: 0.08 (0.35), residues: 259 loop : -2.20 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 255 TYR 0.018 0.001 TYR A 658 PHE 0.014 0.001 PHE A 526 TRP 0.013 0.001 TRP C 37 HIS 0.004 0.001 HIS A 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.18 (14496) covalent geometry : angle 0.56590 / 0.34 (19731) hydrogen bonds : bond 0.16178 / 10.48 ( 495) hydrogen bonds : angle 5.96275 / 4.08 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.354 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 472 TYR cc_start: 0.7203 (t80) cc_final: 0.6966 (t80) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.1149 time to fit residues: 52.9383 Evaluate side-chains 192 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 overall best weight: 0.7326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 ASN A 538 GLN A 576 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN B 151 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.227099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154392 restraints weight = 17842.080| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.47 r_work: 0.3701 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14496 Z= 0.160 Angle : 0.640 10.444 19731 Z= 0.341 Chirality : 0.045 0.285 2183 Planarity : 0.005 0.055 2397 Dihedral : 15.533 175.888 2172 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.50 % Favored : 89.77 % Rotamer: Outliers : 1.05 % Allowed : 9.26 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1642 helix: 1.30 (0.22), residues: 567 sheet: 0.03 (0.33), residues: 273 loop : -2.26 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 744 TYR 0.023 0.002 TYR C 89 PHE 0.023 0.002 PHE A 930 TRP 0.015 0.001 TRP A 470 HIS 0.011 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (14496) covalent geometry : angle 0.64028 / 0.34 (19731) hydrogen bonds : bond 0.05300 / 3.65 ( 495) hydrogen bonds : angle 4.80299 / 3.34 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.436 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: A 168 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6824 (mt-10) REVERT: A 472 TYR cc_start: 0.7170 (t80) cc_final: 0.6898 (t80) REVERT: A 539 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7280 (tttp) REVERT: A 894 ARG cc_start: 0.6385 (ttp80) cc_final: 0.6095 (ttp80) REVERT: A 895 MET cc_start: 0.6574 (ttp) cc_final: 0.5989 (ttp) REVERT: C 129 PHE cc_start: 0.7091 (m-10) cc_final: 0.6845 (m-80) REVERT: C 138 MET cc_start: 0.5982 (ptm) cc_final: 0.5591 (ptm) REVERT: C 160 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5536 (tp) REVERT: C 184 MET cc_start: 0.7171 (mmm) cc_final: 0.6396 (mmm) REVERT: C 188 PHE cc_start: 0.4664 (m-10) cc_final: 0.3662 (m-80) REVERT: C 226 ASP cc_start: 0.7554 (p0) cc_final: 0.6613 (m-30) REVERT: B 15 TYR cc_start: 0.6210 (p90) cc_final: 0.5817 (p90) REVERT: B 167 ARG cc_start: 0.6998 (mtt-85) cc_final: 0.6722 (mtp180) outliers start: 16 outliers final: 7 residues processed: 215 average time/residue: 0.1114 time to fit residues: 33.8375 Evaluate side-chains 173 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 205 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 114 optimal weight: 30.0000 chunk 104 optimal weight: 0.2980 chunk 102 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN A 336 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.225907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153218 restraints weight = 17881.142| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.74 r_work: 0.3622 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14496 Z= 0.154 Angle : 0.615 12.253 19731 Z= 0.326 Chirality : 0.044 0.297 2183 Planarity : 0.005 0.054 2397 Dihedral : 15.502 174.349 2172 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.14 % Favored : 90.13 % Rotamer: Outliers : 2.04 % Allowed : 12.08 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1642 helix: 1.31 (0.22), residues: 562 sheet: -0.06 (0.33), residues: 271 loop : -2.23 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 259 TYR 0.020 0.001 TYR A 658 PHE 0.023 0.002 PHE A 930 TRP 0.013 0.002 TRP A 470 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (14496) covalent geometry : angle 0.61477 / 0.33 (19731) hydrogen bonds : bond 0.04922 / 3.44 ( 495) hydrogen bonds : angle 4.58398 / 3.18 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.425 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: A 539 LYS cc_start: 0.7603 (ttmm) cc_final: 0.7275 (tttp) REVERT: A 895 MET cc_start: 0.6723 (ttp) cc_final: 0.6362 (ttp) REVERT: A 923 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6245 (pt0) REVERT: C 129 PHE cc_start: 0.6973 (m-10) cc_final: 0.6741 (m-80) REVERT: C 184 MET cc_start: 0.7177 (mmm) cc_final: 0.6573 (mmm) REVERT: C 226 ASP cc_start: 0.7546 (p0) cc_final: 0.6590 (m-30) REVERT: C 378 LYS cc_start: 0.8671 (tptp) cc_final: 0.8111 (tptp) REVERT: B 15 TYR cc_start: 0.6252 (p90) cc_final: 0.5764 (p90) outliers start: 31 outliers final: 15 residues processed: 207 average time/residue: 0.1074 time to fit residues: 31.7929 Evaluate side-chains 183 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 937 ASN A 946 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.223865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154493 restraints weight = 17778.532| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.52 r_work: 0.3664 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14496 Z= 0.200 Angle : 0.654 9.787 19731 Z= 0.347 Chirality : 0.046 0.303 2183 Planarity : 0.005 0.057 2397 Dihedral : 15.517 174.311 2172 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.38 % Favored : 89.89 % Rotamer: Outliers : 2.43 % Allowed : 13.59 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.21), residues: 1642 helix: 1.11 (0.22), residues: 560 sheet: -0.21 (0.33), residues: 266 loop : -2.37 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 692 TYR 0.019 0.002 TYR A 658 PHE 0.024 0.002 PHE A 930 TRP 0.017 0.002 TRP A 470 HIS 0.008 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (14496) covalent geometry : angle 0.65439 / 0.35 (19731) hydrogen bonds : bond 0.05390 / 3.76 ( 495) hydrogen bonds : angle 4.64740 / 3.22 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.349 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: A 539 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7543 (tttp) REVERT: A 742 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7593 (mmm160) REVERT: A 856 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6336 (tm-30) REVERT: A 894 ARG cc_start: 0.7411 (ttp80) cc_final: 0.7104 (ttp80) REVERT: A 895 MET cc_start: 0.7149 (ttp) cc_final: 0.6913 (ttp) REVERT: C 129 PHE cc_start: 0.7046 (m-10) cc_final: 0.6684 (m-80) REVERT: C 160 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5413 (tp) REVERT: C 188 PHE cc_start: 0.4369 (m-80) cc_final: 0.3787 (m-80) REVERT: C 226 ASP cc_start: 0.7593 (p0) cc_final: 0.6709 (m-30) REVERT: C 378 LYS cc_start: 0.8728 (tptp) cc_final: 0.8230 (tptp) outliers start: 37 outliers final: 26 residues processed: 212 average time/residue: 0.1012 time to fit residues: 31.5444 Evaluate side-chains 199 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.224502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150712 restraints weight = 18136.292| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.11 r_work: 0.3711 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14496 Z= 0.177 Angle : 0.635 12.086 19731 Z= 0.335 Chirality : 0.044 0.304 2183 Planarity : 0.005 0.068 2397 Dihedral : 15.512 174.204 2172 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.07 % Favored : 90.19 % Rotamer: Outliers : 2.82 % Allowed : 15.17 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.21), residues: 1642 helix: 1.11 (0.22), residues: 558 sheet: -0.29 (0.33), residues: 266 loop : -2.41 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.023 0.002 TYR B 180 PHE 0.023 0.002 PHE A 791 TRP 0.014 0.002 TRP A 470 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (14496) covalent geometry : angle 0.63523 / 0.34 (19731) hydrogen bonds : bond 0.05042 / 3.54 ( 495) hydrogen bonds : angle 4.52981 / 3.13 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.531 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: A 539 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7381 (ttmt) REVERT: A 742 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7923 (mmm160) REVERT: A 751 ASP cc_start: 0.7812 (m-30) cc_final: 0.7561 (t0) REVERT: A 856 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: A 859 MET cc_start: 0.3224 (pmm) cc_final: 0.2747 (ppp) REVERT: A 895 MET cc_start: 0.6931 (ttp) cc_final: 0.6683 (ttp) REVERT: A 922 ILE cc_start: 0.5918 (OUTLIER) cc_final: 0.5694 (mp) REVERT: C 129 PHE cc_start: 0.7002 (m-10) cc_final: 0.6737 (m-80) REVERT: C 210 VAL cc_start: 0.5451 (OUTLIER) cc_final: 0.5232 (p) REVERT: C 226 ASP cc_start: 0.7583 (p0) cc_final: 0.6787 (t0) REVERT: C 378 LYS cc_start: 0.8671 (tptp) cc_final: 0.8131 (tptp) REVERT: B 45 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7459 (mp) REVERT: B 165 ASN cc_start: 0.8144 (t0) cc_final: 0.7728 (t0) outliers start: 43 outliers final: 23 residues processed: 210 average time/residue: 0.1244 time to fit residues: 38.1800 Evaluate side-chains 194 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 937 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.223235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.151265 restraints weight = 18079.543| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.27 r_work: 0.3685 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14496 Z= 0.188 Angle : 0.652 11.404 19731 Z= 0.341 Chirality : 0.045 0.305 2183 Planarity : 0.005 0.065 2397 Dihedral : 15.502 174.229 2172 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.20 % Favored : 90.07 % Rotamer: Outliers : 3.09 % Allowed : 15.50 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.21), residues: 1642 helix: 1.05 (0.22), residues: 555 sheet: -0.35 (0.33), residues: 266 loop : -2.44 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 894 TYR 0.020 0.002 TYR B 180 PHE 0.022 0.002 PHE A 930 TRP 0.015 0.002 TRP A 470 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (14496) covalent geometry : angle 0.65168 / 0.34 (19731) hydrogen bonds : bond 0.05152 / 3.60 ( 495) hydrogen bonds : angle 4.51114 / 3.12 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.590 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: A 267 PHE cc_start: 0.7222 (t80) cc_final: 0.6846 (t80) REVERT: A 539 LYS cc_start: 0.7518 (ttmm) cc_final: 0.7297 (ttmt) REVERT: A 709 ASN cc_start: 0.8309 (t0) cc_final: 0.7958 (t0) REVERT: A 742 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7933 (mmm160) REVERT: A 856 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6294 (tm-30) REVERT: A 859 MET cc_start: 0.3112 (pmm) cc_final: 0.2808 (ppp) REVERT: A 894 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7135 (ttp80) REVERT: A 895 MET cc_start: 0.6976 (ttp) cc_final: 0.6680 (ttp) REVERT: A 922 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5769 (mp) REVERT: C 129 PHE cc_start: 0.7152 (m-10) cc_final: 0.6758 (m-80) REVERT: C 210 VAL cc_start: 0.5474 (OUTLIER) cc_final: 0.5262 (p) REVERT: C 226 ASP cc_start: 0.7720 (p0) cc_final: 0.6850 (t0) REVERT: C 378 LYS cc_start: 0.8678 (tptp) cc_final: 0.8141 (tptp) REVERT: B 45 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7481 (mp) REVERT: B 165 ASN cc_start: 0.8261 (t0) cc_final: 0.7849 (t0) outliers start: 47 outliers final: 32 residues processed: 204 average time/residue: 0.1152 time to fit residues: 34.6255 Evaluate side-chains 201 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 157 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.223422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.155707 restraints weight = 17947.738| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.88 r_work: 0.3712 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14496 Z= 0.166 Angle : 0.627 12.572 19731 Z= 0.329 Chirality : 0.045 0.306 2183 Planarity : 0.005 0.079 2397 Dihedral : 15.490 174.007 2172 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.20 % Favored : 90.13 % Rotamer: Outliers : 2.89 % Allowed : 16.41 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.21), residues: 1642 helix: 1.10 (0.22), residues: 554 sheet: -0.38 (0.34), residues: 260 loop : -2.41 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 255 TYR 0.019 0.001 TYR B 180 PHE 0.021 0.002 PHE A 791 TRP 0.015 0.002 TRP A 8 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (14496) covalent geometry : angle 0.62742 / 0.33 (19731) hydrogen bonds : bond 0.04864 / 3.40 ( 495) hydrogen bonds : angle 4.44645 / 3.07 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.329 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: A 28 GLU cc_start: 0.7085 (tt0) cc_final: 0.6549 (tp30) REVERT: A 218 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: A 709 ASN cc_start: 0.8355 (t0) cc_final: 0.8012 (t0) REVERT: A 751 ASP cc_start: 0.7859 (m-30) cc_final: 0.7628 (t0) REVERT: A 859 MET cc_start: 0.2961 (pmm) cc_final: 0.2533 (ppp) REVERT: A 894 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7220 (ttp80) REVERT: A 895 MET cc_start: 0.7126 (ttp) cc_final: 0.6837 (ttp) REVERT: A 922 ILE cc_start: 0.6031 (OUTLIER) cc_final: 0.5752 (mp) REVERT: C 21 ARG cc_start: 0.5987 (mmp-170) cc_final: 0.5597 (mmp-170) REVERT: C 22 PHE cc_start: 0.5391 (p90) cc_final: 0.5163 (p90) REVERT: C 129 PHE cc_start: 0.7091 (m-10) cc_final: 0.6720 (m-80) REVERT: C 226 ASP cc_start: 0.7681 (p0) cc_final: 0.6938 (t0) REVERT: C 378 LYS cc_start: 0.8659 (tptp) cc_final: 0.8134 (tptp) REVERT: B 15 TYR cc_start: 0.6449 (p90) cc_final: 0.6093 (p90) REVERT: B 45 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7502 (mp) REVERT: B 165 ASN cc_start: 0.8112 (t0) cc_final: 0.7791 (t0) outliers start: 44 outliers final: 34 residues processed: 212 average time/residue: 0.1127 time to fit residues: 35.0634 Evaluate side-chains 205 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 13 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 142 optimal weight: 0.0030 chunk 16 optimal weight: 0.4980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.225639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.155114 restraints weight = 18091.143| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.11 r_work: 0.3730 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14496 Z= 0.126 Angle : 0.607 10.811 19731 Z= 0.318 Chirality : 0.043 0.309 2183 Planarity : 0.004 0.058 2397 Dihedral : 15.453 173.735 2172 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.83 % Favored : 90.50 % Rotamer: Outliers : 2.76 % Allowed : 16.81 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.21), residues: 1642 helix: 1.24 (0.23), residues: 553 sheet: -0.30 (0.34), residues: 264 loop : -2.35 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 255 TYR 0.018 0.001 TYR A 658 PHE 0.022 0.002 PHE C 152 TRP 0.015 0.001 TRP A 8 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (14496) covalent geometry : angle 0.60714 / 0.32 (19731) hydrogen bonds : bond 0.04237 / 2.97 ( 495) hydrogen bonds : angle 4.34747 / 3.00 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.555 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: A 28 GLU cc_start: 0.7067 (tt0) cc_final: 0.6510 (tp30) REVERT: A 267 PHE cc_start: 0.7312 (t80) cc_final: 0.7050 (t80) REVERT: A 539 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7785 (tttp) REVERT: A 709 ASN cc_start: 0.8324 (t0) cc_final: 0.7969 (t0) REVERT: A 895 MET cc_start: 0.7015 (ttp) cc_final: 0.6563 (ttp) REVERT: A 922 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5606 (mp) REVERT: C 129 PHE cc_start: 0.7124 (m-10) cc_final: 0.6799 (m-80) REVERT: C 226 ASP cc_start: 0.7497 (p0) cc_final: 0.6868 (t0) REVERT: C 378 LYS cc_start: 0.8652 (tptp) cc_final: 0.8121 (tptp) REVERT: B 15 TYR cc_start: 0.6406 (p90) cc_final: 0.6007 (p90) REVERT: B 45 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7498 (mp) REVERT: B 165 ASN cc_start: 0.8125 (t0) cc_final: 0.7771 (t0) outliers start: 42 outliers final: 30 residues processed: 208 average time/residue: 0.1222 time to fit residues: 37.2036 Evaluate side-chains 197 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 32 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.223600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152751 restraints weight = 18085.980| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.69 r_work: 0.3675 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14496 Z= 0.163 Angle : 0.647 12.665 19731 Z= 0.338 Chirality : 0.045 0.311 2183 Planarity : 0.004 0.044 2397 Dihedral : 15.477 173.788 2172 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.50 % Favored : 89.89 % Rotamer: Outliers : 2.56 % Allowed : 17.33 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.21), residues: 1642 helix: 1.12 (0.22), residues: 558 sheet: -0.32 (0.34), residues: 260 loop : -2.48 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 894 TYR 0.018 0.002 TYR A 658 PHE 0.026 0.002 PHE C 272 TRP 0.013 0.002 TRP A 470 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (14496) covalent geometry : angle 0.64698 / 0.34 (19731) hydrogen bonds : bond 0.04695 / 3.28 ( 495) hydrogen bonds : angle 4.39371 / 3.04 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7115 (tt0) cc_final: 0.6526 (tp30) REVERT: A 218 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: A 539 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7717 (tttp) REVERT: A 709 ASN cc_start: 0.8347 (t0) cc_final: 0.8046 (t0) REVERT: A 894 ARG cc_start: 0.7475 (ttp80) cc_final: 0.7152 (ttp80) REVERT: A 895 MET cc_start: 0.7090 (ttp) cc_final: 0.6819 (ttp) REVERT: A 922 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5692 (mp) REVERT: C 129 PHE cc_start: 0.7223 (m-10) cc_final: 0.6957 (m-80) REVERT: C 226 ASP cc_start: 0.7660 (p0) cc_final: 0.6942 (t0) REVERT: C 255 ARG cc_start: 0.7136 (mmp-170) cc_final: 0.6560 (mmm160) REVERT: C 378 LYS cc_start: 0.8684 (tptp) cc_final: 0.8141 (tptp) REVERT: B 15 TYR cc_start: 0.6455 (p90) cc_final: 0.6001 (p90) REVERT: B 45 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7478 (mp) REVERT: B 165 ASN cc_start: 0.8141 (t0) cc_final: 0.7793 (t0) outliers start: 39 outliers final: 32 residues processed: 195 average time/residue: 0.1160 time to fit residues: 32.7297 Evaluate side-chains 197 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 4 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 73 optimal weight: 0.0770 chunk 79 optimal weight: 0.0870 chunk 109 optimal weight: 0.9980 chunk 37 optimal weight: 0.0170 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 963 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.226563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.159310 restraints weight = 18157.626| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.28 r_work: 0.3750 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14496 Z= 0.120 Angle : 0.607 9.840 19731 Z= 0.318 Chirality : 0.043 0.312 2183 Planarity : 0.004 0.047 2397 Dihedral : 15.438 173.418 2172 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.59 % Favored : 90.80 % Rotamer: Outliers : 2.36 % Allowed : 17.60 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.21), residues: 1642 helix: 1.29 (0.23), residues: 553 sheet: -0.31 (0.33), residues: 269 loop : -2.39 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 742 TYR 0.016 0.001 TYR A 658 PHE 0.020 0.001 PHE A 930 TRP 0.017 0.001 TRP A 8 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (14496) covalent geometry : angle 0.60710 / 0.32 (19731) hydrogen bonds : bond 0.03945 / 2.76 ( 495) hydrogen bonds : angle 4.31829 / 2.98 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3284 Ramachandran restraints generated. 1642 Oldfield, 0 Emsley, 1642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7039 (tt0) cc_final: 0.6503 (tp30) REVERT: A 97 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6972 (mmm-85) REVERT: A 218 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: A 357 MET cc_start: 0.1699 (ttt) cc_final: 0.1454 (tmm) REVERT: A 539 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7708 (tttp) REVERT: A 709 ASN cc_start: 0.8361 (t0) cc_final: 0.8021 (t0) REVERT: A 895 MET cc_start: 0.7103 (ttp) cc_final: 0.6673 (ttp) REVERT: A 922 ILE cc_start: 0.5888 (OUTLIER) cc_final: 0.5580 (mp) REVERT: C 129 PHE cc_start: 0.7167 (m-10) cc_final: 0.6867 (m-10) REVERT: C 226 ASP cc_start: 0.7442 (p0) cc_final: 0.6834 (t0) REVERT: C 255 ARG cc_start: 0.7106 (mmp-170) cc_final: 0.6558 (mmm160) REVERT: C 378 LYS cc_start: 0.8653 (tptp) cc_final: 0.8130 (tptp) REVERT: B 15 TYR cc_start: 0.6417 (p90) cc_final: 0.6026 (p90) REVERT: B 45 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7442 (mp) REVERT: B 165 ASN cc_start: 0.8104 (t0) cc_final: 0.7725 (t0) outliers start: 36 outliers final: 24 residues processed: 199 average time/residue: 0.1171 time to fit residues: 33.9374 Evaluate side-chains 194 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 22 optimal weight: 0.0370 chunk 71 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 963 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.226329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.158992 restraints weight = 18116.681| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.48 r_work: 0.3746 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14496 Z= 0.126 Angle : 0.615 12.973 19731 Z= 0.321 Chirality : 0.044 0.314 2183 Planarity : 0.004 0.045 2397 Dihedral : 15.427 173.407 2172 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.26 % Favored : 90.13 % Rotamer: Outliers : 2.10 % Allowed : 17.53 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.21), residues: 1642 helix: 1.27 (0.23), residues: 553 sheet: -0.38 (0.33), residues: 273 loop : -2.35 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 742 TYR 0.021 0.001 TYR A 723 PHE 0.022 0.002 PHE A 930 TRP 0.013 0.001 TRP A 8 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14496) covalent geometry : angle 0.61516 / 0.32 (19731) hydrogen bonds : bond 0.04027 / 2.80 ( 495) hydrogen bonds : angle 4.33107 / 3.00 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4287.11 seconds wall clock time: 73 minutes 49.22 seconds (4429.22 seconds total)