Starting phenix.real_space_refine on Sun Nov 17 15:57:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpa_34929/11_2024/8hpa_34929.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpa_34929/11_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpa_34929/11_2024/8hpa_34929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpa_34929/11_2024/8hpa_34929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpa_34929/11_2024/8hpa_34929.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpa_34929/11_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-5513/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: 9.45, per 1000 atoms: 0.67 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: 3.60 Conformation dependent library (CDL) restraints added in 1.9 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: 4.68 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: 4.79 Time building geometry restraints manager: 4.16 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: 4.360 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.270 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.640 ------------------------------------------------------------------------------- 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 : 1.603 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: 0.3242 time to fit residues: 146.8162 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 : 1.547 ------------------------------------------------------------------------------- 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 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: