Starting phenix.real_space_refine on Mon Dec 30 21:51:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpa_34929/12_2024/8hpa_34929.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpa_34929/12_2024/8hpa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpa_34929/12_2024/8hpa_34929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpa_34929/12_2024/8hpa_34929.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpa_34929/12_2024/8hpa_34929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpa_34929/12_2024/8hpa_34929.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.91, per 1000 atoms: 0.63 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: 3.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 5.27 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: 4.83 Time building geometry restraints manager: 3.98 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=" O3' DT D -6 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" C GLN C 146 " pdb=" N SER C 147 " ideal model delta sigma weight residual 1.331 1.356 -0.025 2.07e-02 2.33e+03 1.47e+00 bond pdb=" N LEU A 889 " pdb=" CA LEU A 889 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.36e+00 bond pdb=" C3' DA E -2 " pdb=" O3' DA E -2 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" C SER B 43 " pdb=" N PRO B 44 " ideal model delta sigma weight residual 1.332 1.347 -0.015 1.32e-02 5.74e+03 1.32e+00 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 19439 1.95 - 3.91: 249 3.91 - 5.86: 37 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=" C GLN C 146 " pdb=" N SER C 147 " pdb=" CA SER C 147 " ideal model delta sigma weight residual 121.80 131.57 -9.77 2.44e+00 1.68e-01 1.60e+01 angle pdb=" C HIS B 8 " pdb=" N ALA B 9 " pdb=" CA ALA B 9 " ideal model delta sigma weight residual 121.80 131.43 -9.63 2.44e+00 1.68e-01 1.56e+01 angle pdb=" CA SER A 884 " pdb=" C SER A 884 " pdb=" N SER A 885 " ideal model delta sigma weight residual 119.98 117.12 2.86 8.50e-01 1.38e+00 1.13e+01 angle pdb=" N ILE A 966 " pdb=" CA ILE A 966 " pdb=" C ILE A 966 " ideal model delta sigma weight residual 106.42 111.44 -5.02 1.51e+00 4.39e-01 1.10e+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: 1335 0.030 - 0.059: 576 0.059 - 0.089: 159 0.089 - 0.119: 89 0.119 - 0.148: 24 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=" CA GLU B 203 " pdb=" N GLU B 203 " pdb=" C GLU B 203 " pdb=" CB GLU B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-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: 2.640 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: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 36.090 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14496 Z= 0.151 Angle : 0.545 9.769 19731 Z= 0.296 Chirality : 0.040 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (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 TRP 0.013 0.001 TRP C 37 HIS 0.004 0.001 HIS A 897 PHE 0.014 0.001 PHE A 526 TYR 0.018 0.001 TYR A 658 ARG 0.005 0.000 ARG C 255 *********************** 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 : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 TYR cc_start: 0.7203 (t80) cc_final: 0.6965 (t80) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.3307 time to fit residues: 149.6495 Evaluate side-chains 193 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 0.0670 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 322 ASN A 538 GLN A 576 ASN A 937 ASN ** C 9 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14496 Z= 0.315 Angle : 0.666 10.079 19731 Z= 0.353 Chirality : 0.046 0.213 2183 Planarity : 0.005 0.050 2397 Dihedral : 15.596 176.518 2172 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.74 % Favored : 89.52 % Rotamer: Outliers : 1.38 % Allowed : 10.44 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1642 helix: 1.17 (0.22), residues: 564 sheet: 0.02 (0.35), residues: 260 loop : -2.31 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 470 HIS 0.011 0.002 HIS B 181 PHE 0.023 0.002 PHE A 200 TYR 0.020 0.002 TYR A 658 ARG 0.005 0.001 ARG A 744 *********************** 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 222 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 MET cc_start: 0.7446 (mtp) cc_final: 0.7129 (mtp) REVERT: C 184 MET cc_start: 0.6917 (mmm) cc_final: 0.6211 (mmm) REVERT: C 188 PHE cc_start: 0.4028 (m-80) cc_final: 0.3790 (m-80) REVERT: B 1 MET cc_start: 0.7519 (pmm) cc_final: 0.7308 (pmm) outliers start: 21 outliers final: 12 residues processed: 218 average time/residue: 0.3043 time to fit residues: 93.7510 Evaluate side-chains 177 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 130 GLN 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 718 LEU Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 937 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN B 147 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14496 Z= 0.216 Angle : 0.607 11.000 19731 Z= 0.320 Chirality : 0.043 0.215 2183 Planarity : 0.004 0.056 2397 Dihedral : 15.523 176.195 2172 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.89 % Favored : 90.38 % Rotamer: Outliers : 2.17 % Allowed : 12.61 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1642 helix: 1.30 (0.23), residues: 559 sheet: 0.08 (0.34), residues: 266 loop : -2.33 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 8 HIS 0.004 0.001 HIS A 170 PHE 0.022 0.002 PHE A 930 TYR 0.030 0.001 TYR C 89 ARG 0.006 0.000 ARG A 894 *********************** 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 219 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 MET cc_start: 0.7400 (mtp) cc_final: 0.7101 (mtp) REVERT: A 709 ASN cc_start: 0.8146 (t0) cc_final: 0.7773 (t0) REVERT: B 1 MET cc_start: 0.7632 (pmm) cc_final: 0.7293 (pmm) outliers start: 33 outliers final: 16 residues processed: 209 average time/residue: 0.3254 time to fit residues: 99.1997 Evaluate side-chains 180 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 512 GLU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 143 LEU 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 148 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 42 optimal weight: 0.0370 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 214 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14496 Z= 0.205 Angle : 0.601 10.548 19731 Z= 0.315 Chirality : 0.043 0.270 2183 Planarity : 0.004 0.053 2397 Dihedral : 15.480 176.194 2172 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.95 % Favored : 90.32 % Rotamer: Outliers : 2.69 % Allowed : 14.45 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1642 helix: 1.25 (0.23), residues: 562 sheet: -0.05 (0.33), residues: 267 loop : -2.32 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 8 HIS 0.004 0.001 HIS A 170 PHE 0.026 0.002 PHE A 791 TYR 0.023 0.001 TYR C 89 ARG 0.008 0.000 ARG A 894 *********************** 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 220 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.2228 (ttt) cc_final: 0.1994 (tmm) REVERT: A 443 MET cc_start: 0.7218 (mtp) cc_final: 0.6991 (mtp) REVERT: A 709 ASN cc_start: 0.8170 (t0) cc_final: 0.7807 (t0) REVERT: A 922 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6292 (mp) outliers start: 41 outliers final: 24 residues processed: 210 average time/residue: 0.2860 time to fit residues: 86.7713 Evaluate side-chains 187 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 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 512 GLU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 718 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 130 VAL 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 C residue 413 ILE 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 132 optimal weight: 0.0050 chunk 90 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 0 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 chunk 143 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14496 Z= 0.186 Angle : 0.591 10.720 19731 Z= 0.309 Chirality : 0.042 0.268 2183 Planarity : 0.004 0.052 2397 Dihedral : 15.411 176.172 2172 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.71 % Favored : 90.56 % Rotamer: Outliers : 2.56 % Allowed : 15.63 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1642 helix: 1.33 (0.23), residues: 561 sheet: -0.11 (0.33), residues: 270 loop : -2.30 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 8 HIS 0.003 0.001 HIS B 181 PHE 0.019 0.001 PHE A 791 TYR 0.020 0.001 TYR C 89 ARG 0.006 0.000 ARG A 894 *********************** 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 207 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: A 692 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7416 (ttm110) REVERT: A 922 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6187 (mp) outliers start: 39 outliers final: 25 residues processed: 198 average time/residue: 0.2826 time to fit residues: 80.9724 Evaluate side-chains 190 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 76 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 326 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR 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 543 ASN Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 718 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 130 VAL 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 413 ILE 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 53 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 0.0370 chunk 83 optimal weight: 3.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14496 Z= 0.302 Angle : 0.667 13.235 19731 Z= 0.347 Chirality : 0.045 0.256 2183 Planarity : 0.005 0.050 2397 Dihedral : 15.440 176.299 2172 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.29 % Favored : 88.98 % Rotamer: Outliers : 2.76 % Allowed : 16.22 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1642 helix: 1.05 (0.22), residues: 561 sheet: -0.19 (0.33), residues: 265 loop : -2.45 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 470 HIS 0.004 0.001 HIS A 461 PHE 0.023 0.002 PHE A 791 TYR 0.018 0.002 TYR A 300 ARG 0.005 0.000 ARG A 97 *********************** 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 210 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 1.583 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 218 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: A 709 ASN cc_start: 0.8164 (t0) cc_final: 0.7588 (t0) REVERT: A 922 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6341 (mp) REVERT: C 22 PHE cc_start: 0.6467 (p90) cc_final: 0.6255 (p90) outliers start: 42 outliers final: 31 residues processed: 202 average time/residue: 0.2844 time to fit residues: 83.3720 Evaluate side-chains 190 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 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 311 CYS Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR 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 543 ASN 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 707 LEU Chi-restraints excluded: chain A residue 718 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 130 VAL 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 C residue 271 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 161 THR 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 153 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 116 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14496 Z= 0.258 Angle : 0.636 12.300 19731 Z= 0.333 Chirality : 0.044 0.257 2183 Planarity : 0.004 0.049 2397 Dihedral : 15.411 175.869 2172 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.81 % Favored : 89.46 % Rotamer: Outliers : 3.28 % Allowed : 16.22 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1642 helix: 1.08 (0.22), residues: 559 sheet: -0.39 (0.33), residues: 268 loop : -2.47 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 470 HIS 0.003 0.001 HIS A 461 PHE 0.021 0.002 PHE C 272 TYR 0.018 0.002 TYR A 668 ARG 0.012 0.000 ARG C 255 *********************** 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 215 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: A 709 ASN cc_start: 0.8207 (t0) cc_final: 0.7644 (t0) REVERT: A 922 ILE cc_start: 0.6651 (OUTLIER) cc_final: 0.6348 (mp) REVERT: C 22 PHE cc_start: 0.6423 (p90) cc_final: 0.6223 (p90) REVERT: C 98 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5980 (mm) outliers start: 50 outliers final: 35 residues processed: 207 average time/residue: 0.2780 time to fit residues: 84.2231 Evaluate side-chains 196 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 170 HIS 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 311 CYS Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 391 THR 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 543 ASN 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 707 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 774 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 C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 226 ASP 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 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 63 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3877 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= 0.197 Angle : 0.619 11.837 19731 Z= 0.322 Chirality : 0.043 0.249 2183 Planarity : 0.004 0.048 2397 Dihedral : 15.355 175.448 2172 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.87 % Favored : 89.40 % Rotamer: Outliers : 3.02 % Allowed : 16.81 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1642 helix: 1.17 (0.22), residues: 559 sheet: -0.36 (0.33), residues: 268 loop : -2.43 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 37 HIS 0.003 0.001 HIS B 181 PHE 0.022 0.002 PHE A 930 TYR 0.018 0.001 TYR A 658 ARG 0.008 0.000 ARG C 255 *********************** 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 208 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6911 (pt0) REVERT: A 218 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: A 443 MET cc_start: 0.7353 (mtp) cc_final: 0.7132 (mtp) REVERT: A 859 MET cc_start: 0.1891 (pmm) cc_final: -0.0631 (mpp) REVERT: A 922 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6354 (mp) REVERT: C 98 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6084 (mm) outliers start: 46 outliers final: 36 residues processed: 198 average time/residue: 0.2962 time to fit residues: 85.2155 Evaluate side-chains 195 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 70 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL 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 311 CYS 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 512 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 545 VAL 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 774 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 C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 413 ILE 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 152 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 148 optimal weight: 0.0270 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14496 Z= 0.244 Angle : 0.640 11.783 19731 Z= 0.334 Chirality : 0.044 0.239 2183 Planarity : 0.004 0.046 2397 Dihedral : 15.373 175.552 2172 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.11 % Favored : 89.22 % Rotamer: Outliers : 3.15 % Allowed : 16.61 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1642 helix: 1.09 (0.22), residues: 560 sheet: -0.37 (0.34), residues: 267 loop : -2.50 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 37 HIS 0.004 0.001 HIS B 8 PHE 0.019 0.002 PHE A 930 TYR 0.018 0.002 TYR A 658 ARG 0.005 0.000 ARG C 255 *********************** 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 205 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6962 (pt0) REVERT: A 218 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: A 540 MET cc_start: 0.6172 (mmt) cc_final: 0.5857 (mtt) REVERT: A 859 MET cc_start: 0.1496 (pmm) cc_final: -0.0836 (mpp) REVERT: A 922 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6355 (mp) REVERT: C 98 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6108 (mm) REVERT: C 166 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6530 (mp) outliers start: 48 outliers final: 38 residues processed: 200 average time/residue: 0.2939 time to fit residues: 87.6557 Evaluate side-chains 192 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 70 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 170 HIS 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 311 CYS 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 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 707 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 774 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 C residue 98 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 413 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 156 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14496 Z= 0.326 Angle : 0.692 12.943 19731 Z= 0.361 Chirality : 0.045 0.241 2183 Planarity : 0.005 0.055 2397 Dihedral : 15.444 175.647 2172 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.67 % Allowed : 11.21 % Favored : 88.12 % Rotamer: Outliers : 2.95 % Allowed : 16.87 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1642 helix: 1.01 (0.22), residues: 552 sheet: -0.51 (0.33), residues: 267 loop : -2.57 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 37 HIS 0.004 0.001 HIS B 133 PHE 0.023 0.002 PHE A 791 TYR 0.020 0.002 TYR A 472 ARG 0.007 0.001 ARG A 742 ********************** 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: 45 poor density : 161 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7090 (pt0) REVERT: A 218 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: A 692 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7415 (mtt90) REVERT: A 742 ARG cc_start: 0.7667 (mmm160) cc_final: 0.7355 (mmm160) REVERT: A 859 MET cc_start: 0.1329 (pmm) cc_final: -0.0858 (mpp) REVERT: A 908 MET cc_start: 0.7768 (tmm) cc_final: 0.7532 (tmm) REVERT: A 922 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6410 (mp) REVERT: B 39 ARG cc_start: 0.5944 (ptt180) cc_final: 0.5731 (ptt180) outliers start: 45 outliers final: 36 residues processed: 200 average time/residue: 0.2775 time to fit residues: 81.1920 Evaluate side-chains 199 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 70 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 170 HIS 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 311 CYS 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 486 TYR 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 707 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 774 LEU 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 C residue 130 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 413 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 139 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 19 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 131 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.224652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.156659 restraints weight = 18081.271| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.16 r_work: 0.3743 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 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 = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4334 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= 0.180 Angle : 0.622 10.891 19731 Z= 0.325 Chirality : 0.043 0.239 2183 Planarity : 0.004 0.047 2397 Dihedral : 15.355 174.636 2172 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.62 % Favored : 89.77 % Rotamer: Outliers : 2.43 % Allowed : 17.86 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1642 helix: 1.22 (0.22), residues: 552 sheet: -0.34 (0.34), residues: 262 loop : -2.51 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 212 HIS 0.003 0.001 HIS A 461 PHE 0.020 0.001 PHE A 930 TYR 0.025 0.001 TYR C 89 ARG 0.008 0.000 ARG A 742 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.91 seconds wall clock time: 61 minutes 37.31 seconds (3697.31 seconds total)